fileRegex not in configNone, using default
WARNING: Less than 30 IDs in DROP_GROUP group1
gnomAD not in configNone, using default
check for missing R packages
AberrantExpression has been turned off in the config file
Found files in scope of wBuild: ['/nas/weka.gel.zone/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/Scripts/AberrantSplicing/pipeline/Counting/00_define_datasets_from_anno.R', '/nas/weka.gel.zone/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/Scripts/AberrantSplicing/pipeline/Counting/01_0_countRNA_init.R', '/nas/weka.gel.zone/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/Scripts/AberrantSplicing/pipeline/Counting/01_1_countRNA_splitReads_samplewise.R', '/nas/weka.gel.zone/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/Scripts/AberrantSplicing/pipeline/Counting/01_2_countRNA_splitReads_merge.R', '/nas/weka.gel.zone/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/Scripts/AberrantSplicing/pipeline/Counting/01_3_countRNA_nonSplitReads_samplewise.R', '/nas/weka.gel.zone/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/Scripts/AberrantSplicing/pipeline/Counting/01_4_countRNA_nonSplitReads_merge.R', '/nas/weka.gel.zone/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/Scripts/AberrantSplicing/pipeline/Counting/01_5_countRNA_collect.R', '/nas/weka.gel.zone/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/Scripts/AberrantSplicing/pipeline/Counting/02_psi_value_calculation_FraseR.R', '/nas/weka.gel.zone/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/Scripts/AberrantSplicing/pipeline/Counting/03_filter_expression_FraseR.R', '/nas/weka.gel.zone/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/Scripts/AberrantSplicing/pipeline/Counting/DatasetsF.R', '/nas/weka.gel.zone/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/Scripts/AberrantSplicing/pipeline/Counting/Summary.R', '/nas/weka.gel.zone/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/Scripts/AberrantSplicing/pipeline/Counting/exportCounts.R', '/nas/weka.gel.zone/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/Scripts/AberrantSplicing/pipeline/FRASER/04_fit_hyperparameters_FraseR.R', '/nas/weka.gel.zone/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/Scripts/AberrantSplicing/pipeline/FRASER/05_fit_autoencoder_FraseR.R', '/nas/weka.gel.zone/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/Scripts/AberrantSplicing/pipeline/FRASER/06_calculation_stats_AE_FraseR.R', '/nas/weka.gel.zone/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/Scripts/AberrantSplicing/pipeline/FRASER/07_extract_results_FraseR.R', '/nas/weka.gel.zone/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/Scripts/AberrantSplicing/pipeline/FRASER/Datasets.R', '/nas/weka.gel.zone/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/Scripts/AberrantSplicing/pipeline/FRASER/Summary.R', '/nas/weka.gel.zone/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/Scripts/AberrantSplicing/pipeline/config.R'].

Got ---
 title: Create datasets from annotation file
 author: Christian Mertes, mumichae
 wb:
  log:
    - snakemake: '`sm str(tmp_dir / "AS" / "{dataset}" / "00_defineDataset.Rds")`'
  params:
    - setup: '`sm cfg.AS.getWorkdir() + "/config.R"`'
    - ids: '`sm lambda w: sa.getIDsByGroup(w.dataset, assay="RNA")`'
    - fileMappingFile: '`sm cfg.getRoot() + "/file_mapping.csv"`'
  input:
    - sampleAnnoFile: '`sm config["sampleAnnotation"]`'
  output:
    - colData: '`sm cfg.getProcessedDataDir() +
                    "/aberrant_splicing/annotations/{dataset}.tsv"`'
    - wBhtml:  '`sm config["htmlOutputPath"] +
                    "/AberrantSplicing/annotations/{dataset}.html"`'
  type: noindex
 output:
  html_document:
   code_folding: hide
   code_download: TRUE
---as a result of parsing YAML header from /nas/weka.gel.zone/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/Scripts/AberrantSplicing/pipeline/Counting/00_define_datasets_from_anno.R.

Parsed params: {'title': 'Create datasets from annotation file', 'author': 'Christian Mertes, mumichae', 'wb': {'log': [{'snakemake': '`sm str(tmp_dir / "AS" / "{dataset}" / "00_defineDataset.Rds")`'}], 'params': [{'setup': '`sm cfg.AS.getWorkdir() + "/config.R"`'}, {'ids': '`sm lambda w: sa.getIDsByGroup(w.dataset, assay="RNA")`'}, {'fileMappingFile': '`sm cfg.getRoot() + "/file_mapping.csv"`'}], 'input': [{'sampleAnnoFile': '`sm config["sampleAnnotation"]`'}], 'output': [{'colData': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/annotations/{dataset}.tsv"`'}, {'wBhtml': '`sm config["htmlOutputPath"] + "/AberrantSplicing/annotations/{dataset}.html"`'}], 'type': 'noindex'}, 'output': {'html_document': {'code_folding': 'hide', 'code_download': True}}}
.
Got ---
 title: Initialize Counting
 author: Luise Schuller
 wb:
  log:
    - snakemake: '`sm str(tmp_dir / "AS" / "{dataset}" / "01_0_init.Rds")`'
  params:
   - setup: '`sm cfg.AS.getWorkdir() + "/config.R"`'
   - workingDir: '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/"`'
  input:
    - colData: '`sm cfg.getProcessedDataDir() +
                    "/aberrant_splicing/annotations/{dataset}.tsv"`'
  output:
   - fdsobj:  '`sm cfg.getProcessedDataDir() +
                   "/aberrant_splicing/datasets/savedObjects/raw-local-{dataset}/fds-object.RDS"`'
   - done_fds: '`sm cfg.getProcessedDataDir() +
                "/aberrant_splicing/datasets/cache/raw-local-{dataset}/fds.done" `'
  type: script
---as a result of parsing YAML header from /nas/weka.gel.zone/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/Scripts/AberrantSplicing/pipeline/Counting/01_0_countRNA_init.R.

Parsed params: {'title': 'Initialize Counting', 'author': 'Luise Schuller', 'wb': {'log': [{'snakemake': '`sm str(tmp_dir / "AS" / "{dataset}" / "01_0_init.Rds")`'}], 'params': [{'setup': '`sm cfg.AS.getWorkdir() + "/config.R"`'}, {'workingDir': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/"`'}], 'input': [{'colData': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/annotations/{dataset}.tsv"`'}], 'output': [{'fdsobj': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/savedObjects/raw-local-{dataset}/fds-object.RDS"`'}, {'done_fds': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/cache/raw-local-{dataset}/fds.done" `'}], 'type': 'script'}}
.
Got ---
 title: Count Split Reads
 author: Luise Schuller
 wb:
  log:
    - snakemake: '`sm str(tmp_dir / "AS" / "{dataset}" / "splitReads" / "{sample_id}.Rds")`'
  params:
   - setup: '`sm cfg.AS.getWorkdir() + "/config.R"`'
   - workingDir: '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/"`'
  input:
   - done_fds: '`sm cfg.getProcessedDataDir() +
                "/aberrant_splicing/datasets/cache/raw-local-{dataset}/fds.done"`'
  output:
   - done_sample_splitCounts: '`sm cfg.getProcessedDataDir() +
                "/aberrant_splicing/datasets/cache/raw-local-{dataset}"
                +"/sample_tmp/splitCounts/sample_{sample_id}.done"`'
  threads: 3
  type: script
---as a result of parsing YAML header from /nas/weka.gel.zone/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/Scripts/AberrantSplicing/pipeline/Counting/01_1_countRNA_splitReads_samplewise.R.

Parsed params: {'title': 'Count Split Reads', 'author': 'Luise Schuller', 'wb': {'log': [{'snakemake': '`sm str(tmp_dir / "AS" / "{dataset}" / "splitReads" / "{sample_id}.Rds")`'}], 'params': [{'setup': '`sm cfg.AS.getWorkdir() + "/config.R"`'}, {'workingDir': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/"`'}], 'input': [{'done_fds': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/cache/raw-local-{dataset}/fds.done"`'}], 'output': [{'done_sample_splitCounts': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/cache/raw-local-{dataset}" +"/sample_tmp/splitCounts/sample_{sample_id}.done"`'}], 'threads': 3, 'type': 'script'}}
.
Got ---
 title: Merge Split Counts
 author: Luise Schuller
 wb:
  log:
    - snakemake: '`sm str(tmp_dir / "AS" / "{dataset}" / "01_2_splitReadsMerge.Rds")`'
  params:
   - setup: '`sm cfg.AS.getWorkdir() + "/config.R"`'
   - workingDir: '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets"`'
  threads: 20
  input:
   - sample_counts: '`sm lambda w: cfg.AS.getSplitCountFiles(w.dataset)`'
  output:
   - countsJ: '`sm cfg.getProcessedDataDir() +
                          "/aberrant_splicing/datasets/savedObjects/raw-local-{dataset}/rawCountsJ.h5"`'
   - gRangesSplitCounts: '`sm cfg.getProcessedDataDir() +
                          "/aberrant_splicing/datasets/cache/raw-local-{dataset}/gRanges_splitCounts.rds"`'
   - gRangesNonSplitCounts: '`sm cfg.getProcessedDataDir() +
                          "/aberrant_splicing/datasets/cache/raw-local-{dataset}/gRanges_NonSplitCounts.rds"`'
   - spliceSites: '`sm cfg.getProcessedDataDir() +
                   "/aberrant_splicing/datasets/cache/raw-local-{dataset}/spliceSites_splitCounts.rds"`'
  type: script
---as a result of parsing YAML header from /nas/weka.gel.zone/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/Scripts/AberrantSplicing/pipeline/Counting/01_2_countRNA_splitReads_merge.R.

Parsed params: {'title': 'Merge Split Counts', 'author': 'Luise Schuller', 'wb': {'log': [{'snakemake': '`sm str(tmp_dir / "AS" / "{dataset}" / "01_2_splitReadsMerge.Rds")`'}], 'params': [{'setup': '`sm cfg.AS.getWorkdir() + "/config.R"`'}, {'workingDir': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets"`'}], 'threads': 20, 'input': [{'sample_counts': '`sm lambda w: cfg.AS.getSplitCountFiles(w.dataset)`'}], 'output': [{'countsJ': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/savedObjects/raw-local-{dataset}/rawCountsJ.h5"`'}, {'gRangesSplitCounts': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/cache/raw-local-{dataset}/gRanges_splitCounts.rds"`'}, {'gRangesNonSplitCounts': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/cache/raw-local-{dataset}/gRanges_NonSplitCounts.rds"`'}, {'spliceSites': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/cache/raw-local-{dataset}/spliceSites_splitCounts.rds"`'}], 'type': 'script'}}
.
Got ---
 title: Nonsplit Counts
 author: Luise Schuller
 wb:
  log:
    - snakemake: '`sm str(tmp_dir / "AS" / "{dataset}" / "nonsplitReads" / "{sample_id}.Rds")`'
  params:
   - setup: '`sm cfg.AS.getWorkdir() + "/config.R"`'
   - workingDir: '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets"`'
  input:
   - spliceSites: '`sm cfg.getProcessedDataDir() +
                   "/aberrant_splicing/datasets/cache/raw-local-{dataset}/spliceSites_splitCounts.rds"`'
  output:
   - done_sample_nonSplitCounts : '`sm cfg.getProcessedDataDir() +
                   "/aberrant_splicing/datasets/cache/raw-local-{dataset}/sample_tmp/nonSplitCounts/sample_{sample_id}.done"`'
  threads: 3
  type: script
---as a result of parsing YAML header from /nas/weka.gel.zone/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/Scripts/AberrantSplicing/pipeline/Counting/01_3_countRNA_nonSplitReads_samplewise.R.

Parsed params: {'title': 'Nonsplit Counts', 'author': 'Luise Schuller', 'wb': {'log': [{'snakemake': '`sm str(tmp_dir / "AS" / "{dataset}" / "nonsplitReads" / "{sample_id}.Rds")`'}], 'params': [{'setup': '`sm cfg.AS.getWorkdir() + "/config.R"`'}, {'workingDir': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets"`'}], 'input': [{'spliceSites': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/cache/raw-local-{dataset}/spliceSites_splitCounts.rds"`'}], 'output': [{'done_sample_nonSplitCounts': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/cache/raw-local-{dataset}/sample_tmp/nonSplitCounts/sample_{sample_id}.done"`'}], 'threads': 3, 'type': 'script'}}
.
Got ---
 title: Merge Nonsplit Counts
 author: Luise Schuller
 wb:
  log:
    - snakemake: '`sm str(tmp_dir / "AS" / "{dataset}" / "01_4_nonSplitReadsMerge.Rds")`'
  params:
   - setup: '`sm cfg.AS.getWorkdir() + "/config.R"`'
   - workingDir: '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets"`'
  threads: 20
  input:
   - sample_counts:  '`sm lambda w: cfg.AS.getNonSplitCountFiles(w.dataset)`'
   - gRangesNonSplitCounts: '`sm cfg.getProcessedDataDir() +
                          "/aberrant_splicing/datasets/cache/raw-local-{dataset}/gRanges_NonSplitCounts.rds"`'
  output:
#   - countsSS: '`sm cfg.getProcessedDataDir() +
#                   "/aberrant_splicing/datasets/savedObjects/raw-local-{dataset}/rawCountsSS.h5"`'
   - done:     '`sm cfg.getProcessedDataDir() +
                "/aberrant_splicing/datasets/savedObjects/raw-local-{dataset}/merge_theta.done"`'
  type: script
---as a result of parsing YAML header from /nas/weka.gel.zone/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/Scripts/AberrantSplicing/pipeline/Counting/01_4_countRNA_nonSplitReads_merge.R.

Parsed params: {'title': 'Merge Nonsplit Counts', 'author': 'Luise Schuller', 'wb': {'log': [{'snakemake': '`sm str(tmp_dir / "AS" / "{dataset}" / "01_4_nonSplitReadsMerge.Rds")`'}], 'params': [{'setup': '`sm cfg.AS.getWorkdir() + "/config.R"`'}, {'workingDir': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets"`'}], 'threads': 20, 'input': [{'sample_counts': '`sm lambda w: cfg.AS.getNonSplitCountFiles(w.dataset)`'}, {'gRangesNonSplitCounts': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/cache/raw-local-{dataset}/gRanges_NonSplitCounts.rds"`'}], 'output': [{'done': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/savedObjects/raw-local-{dataset}/merge_theta.done"`'}], 'type': 'script'}}
.
Got ---
 title: Collect all counts to FRASER Object
 author: Luise Schuller
 wb:
  log:
    - snakemake: '`sm str(tmp_dir / "AS" / "{dataset}" / "01_5_collect.Rds")`'
  params:
   - setup: '`sm cfg.AS.getWorkdir() + "/config.R"`'
   - workingDir: '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets"`'
  input:
    - countsSSdone: '`sm cfg.getProcessedDataDir() +
                          "/aberrant_splicing/datasets/savedObjects/raw-local-{dataset}/merge_theta.done"`'
    - gRangesSplitCounts: '`sm cfg.getProcessedDataDir() +
                          "/aberrant_splicing/datasets/cache/raw-local-{dataset}/gRanges_splitCounts.rds"`'
    - spliceSites: '`sm cfg.getProcessedDataDir() +
                          "/aberrant_splicing/datasets/cache/raw-local-{dataset}/spliceSites_splitCounts.rds"`'
  output:
   - counting_done: '`sm cfg.getProcessedDataDir() +
                          "/aberrant_splicing/datasets/savedObjects/raw-local-{dataset}/counting.done" `'
  type: script
---as a result of parsing YAML header from /nas/weka.gel.zone/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/Scripts/AberrantSplicing/pipeline/Counting/01_5_countRNA_collect.R.

Parsed params: {'title': 'Collect all counts to FRASER Object', 'author': 'Luise Schuller', 'wb': {'log': [{'snakemake': '`sm str(tmp_dir / "AS" / "{dataset}" / "01_5_collect.Rds")`'}], 'params': [{'setup': '`sm cfg.AS.getWorkdir() + "/config.R"`'}, {'workingDir': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets"`'}], 'input': [{'countsSSdone': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/savedObjects/raw-local-{dataset}/merge_theta.done"`'}, {'gRangesSplitCounts': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/cache/raw-local-{dataset}/gRanges_splitCounts.rds"`'}, {'spliceSites': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/cache/raw-local-{dataset}/spliceSites_splitCounts.rds"`'}], 'output': [{'counting_done': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/savedObjects/raw-local-{dataset}/counting.done" `'}], 'type': 'script'}}
.
Got ---
 title: Calculate PSI values
 author: Christian Mertes
 wb:
  log:
   - snakemake: '`sm str(tmp_dir / "AS" / "{dataset}" / "02_PSIcalc.Rds")`'
  params:
   - setup: '`sm cfg.AS.getWorkdir() + "/config.R"`'
   - workingDir: '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/"`'
  threads: 30
  input:
   - counting_done: '`sm cfg.getProcessedDataDir() +
                "/aberrant_splicing/datasets/savedObjects/raw-local-{dataset}/counting.done" `'
  output:
  - theta:     '`sm cfg.getProcessedDataDir() +
                    "/aberrant_splicing/datasets/savedObjects/raw-local-{dataset}/theta.h5"`'
  type: script
---as a result of parsing YAML header from /nas/weka.gel.zone/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/Scripts/AberrantSplicing/pipeline/Counting/02_psi_value_calculation_FraseR.R.

Parsed params: {'title': 'Calculate PSI values', 'author': 'Christian Mertes', 'wb': {'log': [{'snakemake': '`sm str(tmp_dir / "AS" / "{dataset}" / "02_PSIcalc.Rds")`'}], 'params': [{'setup': '`sm cfg.AS.getWorkdir() + "/config.R"`'}, {'workingDir': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/"`'}], 'threads': 30, 'input': [{'counting_done': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/savedObjects/raw-local-{dataset}/counting.done" `'}], 'output': [{'theta': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/savedObjects/raw-local-{dataset}/theta.h5"`'}], 'type': 'script'}}
.
Got ---
 title: Filter and clean dataset
 author: Christian Mertes
 wb:
  log:
    - snakemake: '`sm str(tmp_dir / "AS" / "{dataset}" / "03_filter.Rds")`'
  params:
   - setup: '`sm cfg.AS.getWorkdir() + "/config.R"`'
   - workingDir: '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/"`'
   - exCountIDs: '`sm lambda w: sa.getIDsByGroup(w.dataset, assay="SPLICE_COUNT")`'
  input:
   - theta:  '`sm cfg.getProcessedDataDir() +
                  "/aberrant_splicing/datasets/savedObjects/raw-local-{dataset}/theta.h5"`'
   - exCounts: '`sm lambda w: cfg.AS.getExternalCounts(w.dataset, "k_j_counts")`'
  output:
   - fds: '`sm cfg.getProcessedDataDir() +
                  "/aberrant_splicing/datasets/savedObjects/{dataset}/fds-object.RDS"`'
   - done: '`sm cfg.getProcessedDataDir() +
                  "/aberrant_splicing/datasets/savedObjects/{dataset}/filter.done" `'
  threads: 3
  type: script
---as a result of parsing YAML header from /nas/weka.gel.zone/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/Scripts/AberrantSplicing/pipeline/Counting/03_filter_expression_FraseR.R.

Parsed params: {'title': 'Filter and clean dataset', 'author': 'Christian Mertes', 'wb': {'log': [{'snakemake': '`sm str(tmp_dir / "AS" / "{dataset}" / "03_filter.Rds")`'}], 'params': [{'setup': '`sm cfg.AS.getWorkdir() + "/config.R"`'}, {'workingDir': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/"`'}, {'exCountIDs': '`sm lambda w: sa.getIDsByGroup(w.dataset, assay="SPLICE_COUNT")`'}], 'input': [{'theta': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/savedObjects/raw-local-{dataset}/theta.h5"`'}, {'exCounts': '`sm lambda w: cfg.AS.getExternalCounts(w.dataset, "k_j_counts")`'}], 'output': [{'fds': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/savedObjects/{dataset}/fds-object.RDS"`'}, {'done': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/savedObjects/{dataset}/filter.done" `'}], 'threads': 3, 'type': 'script'}}
.
Got ---
 title: FRASER counting analysis over all datasets
 wb:
  log:
    - snakemake: '`sm str(tmp_dir / "AS" / "CountingOverview.Rds")`'
  input:
   - counting_summary: '`sm expand(config["htmlOutputPath"] +
                     "/AberrantSplicing/{dataset}_countSummary.html",
                     dataset=cfg.AS.groups)`'
 output:
  html_document
---as a result of parsing YAML header from /nas/weka.gel.zone/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/Scripts/AberrantSplicing/pipeline/Counting/DatasetsF.R.

Parsed params: {'title': 'FRASER counting analysis over all datasets', 'wb': {'log': [{'snakemake': '`sm str(tmp_dir / "AS" / "CountingOverview.Rds")`'}], 'input': [{'counting_summary': '`sm expand(config["htmlOutputPath"] + "/AberrantSplicing/{dataset}_countSummary.html", dataset=cfg.AS.groups)`'}]}, 'output': 'html_document'}
.
Got ---
 title: "Count Summary: `r gsub('_', ' ', snakemake@wildcards$dataset)`"
 author: Christian Mertes
 wb:
  log:
    - snakemake: '`sm str(tmp_dir / "AS" / "{dataset}" / "CountSummary.Rds")`'
  params:
   - setup: '`sm cfg.AS.getWorkdir() + "/config.R"`'
   - workingDir: '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/"`'
  input:
   - filter: '`sm cfg.getProcessedDataDir() +
                "/aberrant_splicing/datasets/savedObjects/{dataset}/filter.done" `'
  output:
   - wBhtml: '`sm config["htmlOutputPath"] +
                  "/AberrantSplicing/{dataset}_countSummary.html"`'
  type: noindex
---as a result of parsing YAML header from /nas/weka.gel.zone/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/Scripts/AberrantSplicing/pipeline/Counting/Summary.R.

Parsed params: {'title': "Count Summary: `r gsub('_', ' ', snakemake@wildcards$dataset)`", 'author': 'Christian Mertes', 'wb': {'log': [{'snakemake': '`sm str(tmp_dir / "AS" / "{dataset}" / "CountSummary.Rds")`'}], 'params': [{'setup': '`sm cfg.AS.getWorkdir() + "/config.R"`'}, {'workingDir': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/"`'}], 'input': [{'filter': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/savedObjects/{dataset}/filter.done" `'}], 'output': [{'wBhtml': '`sm config["htmlOutputPath"] + "/AberrantSplicing/{dataset}_countSummary.html"`'}], 'type': 'noindex'}}
.
Got ---
 title: Collect all counts from FRASER Object
 author: mumichae, vyepez, c-mertes
 wb:
  log:
    - snakemake: '`sm str(tmp_dir / "AS" / "{dataset}" / "{genomeAssembly}--{annotation}_export.Rds")`'
  params:
   - setup: '`sm cfg.AS.getWorkdir() + "/config.R"`'

  input:
   - annotation: '`sm cfg.getProcessedDataDir() + "/preprocess/{annotation}/txdb.db"`'
   - fds_theta: '`sm cfg.getProcessedDataDir() +
                    "/aberrant_splicing/datasets/savedObjects/raw-local-{dataset}/theta.h5"`'
  output:
    - k_counts: '`sm expand(cfg.exportCounts.getFilePattern(str_=True, expandStr=True) + "/k_{metric}_counts.tsv.gz", metric=["j", "theta"])`'
    - n_counts: '`sm expand(cfg.exportCounts.getFilePattern(str_=True, expandStr=True) + "/n_{metric}_counts.tsv.gz", metric=["psi5", "psi3", "theta"])`'
  type: script
---as a result of parsing YAML header from /nas/weka.gel.zone/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/Scripts/AberrantSplicing/pipeline/Counting/exportCounts.R.

Parsed params: {'title': 'Collect all counts from FRASER Object', 'author': 'mumichae, vyepez, c-mertes', 'wb': {'log': [{'snakemake': '`sm str(tmp_dir / "AS" / "{dataset}" / "{genomeAssembly}--{annotation}_export.Rds")`'}], 'params': [{'setup': '`sm cfg.AS.getWorkdir() + "/config.R"`'}], 'input': [{'annotation': '`sm cfg.getProcessedDataDir() + "/preprocess/{annotation}/txdb.db"`'}, {'fds_theta': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/savedObjects/raw-local-{dataset}/theta.h5"`'}], 'output': [{'k_counts': '`sm expand(cfg.exportCounts.getFilePattern(str_=True, expandStr=True) + "/k_{metric}_counts.tsv.gz", metric=["j", "theta"])`'}, {'n_counts': '`sm expand(cfg.exportCounts.getFilePattern(str_=True, expandStr=True) + "/n_{metric}_counts.tsv.gz", metric=["psi5", "psi3", "theta"])`'}], 'type': 'script'}}
.
Got ---
 title: Hyper parameter optimization
 author: Christian Mertes
 wb:
  log:
    - snakemake: '`sm str(tmp_dir / "AS" / "{dataset}" / "04_hyper.Rds")`'
  params:
   - setup: '`sm cfg.AS.getWorkdir() + "/config.R"`'
   - workingDir: '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/"`'
  threads: 12
  input:
   - filter: '`sm cfg.getProcessedDataDir() +
                "/aberrant_splicing/datasets/savedObjects/{dataset}/filter.done" `'
  output:
   - hyper: '`sm cfg.getProcessedDataDir() +
                "/aberrant_splicing/datasets/savedObjects/{dataset}/hyper.done" `'
  type: script
---as a result of parsing YAML header from /nas/weka.gel.zone/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/Scripts/AberrantSplicing/pipeline/FRASER/04_fit_hyperparameters_FraseR.R.

Parsed params: {'title': 'Hyper parameter optimization', 'author': 'Christian Mertes', 'wb': {'log': [{'snakemake': '`sm str(tmp_dir / "AS" / "{dataset}" / "04_hyper.Rds")`'}], 'params': [{'setup': '`sm cfg.AS.getWorkdir() + "/config.R"`'}, {'workingDir': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/"`'}], 'threads': 12, 'input': [{'filter': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/savedObjects/{dataset}/filter.done" `'}], 'output': [{'hyper': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/savedObjects/{dataset}/hyper.done" `'}], 'type': 'script'}}
.
Got ---
 title: Fitting the autoencoder
 author: Christian Mertes
 wb:
  log:
    - snakemake: '`sm str(tmp_dir / "AS" / "{dataset}" / "05_fit.Rds")`'
  params:
   - setup: '`sm cfg.AS.getWorkdir() + "/config.R"`'
   - workingDir: '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/"`'
  threads: 20
  input:
   - hyper: '`sm cfg.getProcessedDataDir() +
                "/aberrant_splicing/datasets/savedObjects/{dataset}/hyper.done" `'
  output:
   - fdsout: '`sm cfg.getProcessedDataDir() +
                  "/aberrant_splicing/datasets/savedObjects/{dataset}/predictedMeans_theta.h5"`'
  type: script
---as a result of parsing YAML header from /nas/weka.gel.zone/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/Scripts/AberrantSplicing/pipeline/FRASER/05_fit_autoencoder_FraseR.R.

Parsed params: {'title': 'Fitting the autoencoder', 'author': 'Christian Mertes', 'wb': {'log': [{'snakemake': '`sm str(tmp_dir / "AS" / "{dataset}" / "05_fit.Rds")`'}], 'params': [{'setup': '`sm cfg.AS.getWorkdir() + "/config.R"`'}, {'workingDir': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/"`'}], 'threads': 20, 'input': [{'hyper': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/savedObjects/{dataset}/hyper.done" `'}], 'output': [{'fdsout': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/savedObjects/{dataset}/predictedMeans_theta.h5"`'}], 'type': 'script'}}
.
Got ---
 title: Calculate P values
 author: Christian Mertes
 wb:
  log:
    - snakemake: '`sm str(tmp_dir / "AS" / "{dataset}" / "06_stats.Rds")`'
  params:
   - setup: '`sm cfg.AS.getWorkdir() + "/config.R"`'
   - workingDir: '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/"`'
  threads: 20
  input:
   - fdsin:  '`sm cfg.getProcessedDataDir() +
                  "/aberrant_splicing/datasets/savedObjects/{dataset}/" +
                  "predictedMeans_theta.h5"`'
  output:
   - fdsout: '`sm cfg.getProcessedDataDir() +
                  "/aberrant_splicing/datasets/savedObjects/{dataset}/" +
                  "padjBetaBinomial_theta.h5"`'
  type: script
---as a result of parsing YAML header from /nas/weka.gel.zone/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/Scripts/AberrantSplicing/pipeline/FRASER/06_calculation_stats_AE_FraseR.R.

Parsed params: {'title': 'Calculate P values', 'author': 'Christian Mertes', 'wb': {'log': [{'snakemake': '`sm str(tmp_dir / "AS" / "{dataset}" / "06_stats.Rds")`'}], 'params': [{'setup': '`sm cfg.AS.getWorkdir() + "/config.R"`'}, {'workingDir': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/"`'}], 'threads': 20, 'input': [{'fdsin': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/savedObjects/{dataset}/" + "predictedMeans_theta.h5"`'}], 'output': [{'fdsout': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/savedObjects/{dataset}/" + "padjBetaBinomial_theta.h5"`'}], 'type': 'script'}}
.
Got ---
 title: Results of FRASER analysis
 author: Christian Mertes
 wb:
  log:
    - snakemake: '`sm str(tmp_dir / "AS" / "{dataset}--{annotation}" / "07_results.Rds")`'
  params:
   - workingDir: '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/"`'
   - outputDir: '`sm cfg.getProcessedResultsDir() + "/aberrant_splicing/datasets/"`'
   - padjCutoff: '`sm cfg.AS.get("padjCutoff")`'
   - zScoreCutoff: '`sm cfg.AS.get("zScoreCutoff")`'
   - deltaPsiCutoff: '`sm cfg.AS.get("deltaPsiCutoff")`'
   - hpoFile: '`sm cfg.get("hpoFile")`'
  threads: 10
  input:
   - setup: '`sm cfg.AS.getWorkdir() + "/config.R"`'
   - add_HPO_cols: '`sm str(projectDir / ".drop" / "helpers" / "add_HPO_cols.R")`'
   - fdsin: '`sm cfg.getProcessedDataDir() +
                 "/aberrant_splicing/datasets/savedObjects/{dataset}/" +
                 "padjBetaBinomial_theta.h5"`'
   - txdb: '`sm cfg.getProcessedDataDir() + "/preprocess/{annotation}/txdb.db"`'
   - gene_name_mapping: '`sm cfg.getProcessedDataDir() + "/preprocess/{annotation}/gene_name_mapping_{annotation}.tsv"`'
  output:
   - resultTableJunc: '`sm cfg.getProcessedResultsDir() +
                          "/aberrant_splicing/results/{annotation}/fraser/{dataset}/results_per_junction.tsv"`'
   - resultTableGene: '`sm cfg.getProcessedResultsDir() +
                          "/aberrant_splicing/results/{annotation}/fraser/{dataset}/results.tsv"`'
   - fds: '`sm cfg.getProcessedResultsDir() +
                 "/aberrant_splicing/datasets/savedObjects/{dataset}--{annotation}/fds-object.RDS"`'
  type: script
---as a result of parsing YAML header from /nas/weka.gel.zone/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/Scripts/AberrantSplicing/pipeline/FRASER/07_extract_results_FraseR.R.

Parsed params: {'title': 'Results of FRASER analysis', 'author': 'Christian Mertes', 'wb': {'log': [{'snakemake': '`sm str(tmp_dir / "AS" / "{dataset}--{annotation}" / "07_results.Rds")`'}], 'params': [{'workingDir': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/"`'}, {'outputDir': '`sm cfg.getProcessedResultsDir() + "/aberrant_splicing/datasets/"`'}, {'padjCutoff': '`sm cfg.AS.get("padjCutoff")`'}, {'zScoreCutoff': '`sm cfg.AS.get("zScoreCutoff")`'}, {'deltaPsiCutoff': '`sm cfg.AS.get("deltaPsiCutoff")`'}, {'hpoFile': '`sm cfg.get("hpoFile")`'}], 'threads': 10, 'input': [{'setup': '`sm cfg.AS.getWorkdir() + "/config.R"`'}, {'add_HPO_cols': '`sm str(projectDir / ".drop" / "helpers" / "add_HPO_cols.R")`'}, {'fdsin': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/savedObjects/{dataset}/" + "padjBetaBinomial_theta.h5"`'}, {'txdb': '`sm cfg.getProcessedDataDir() + "/preprocess/{annotation}/txdb.db"`'}, {'gene_name_mapping': '`sm cfg.getProcessedDataDir() + "/preprocess/{annotation}/gene_name_mapping_{annotation}.tsv"`'}], 'output': [{'resultTableJunc': '`sm cfg.getProcessedResultsDir() + "/aberrant_splicing/results/{annotation}/fraser/{dataset}/results_per_junction.tsv"`'}, {'resultTableGene': '`sm cfg.getProcessedResultsDir() + "/aberrant_splicing/results/{annotation}/fraser/{dataset}/results.tsv"`'}, {'fds': '`sm cfg.getProcessedResultsDir() + "/aberrant_splicing/datasets/savedObjects/{dataset}--{annotation}/fds-object.RDS"`'}], 'type': 'script'}}
.
Got ---
 title: Full FRASER analysis over all datasets
 wb:
  log:
    - snakemake: '`sm str(tmp_dir / "AS" / "FRASER_datasets.Rds")`'
  input:
   - fraser_summary: '`sm expand(config["htmlOutputPath"] +
                     "/AberrantSplicing/{dataset}--{annotation}_summary.html",
                     annotation=cfg.genome.getGeneVersions(), dataset=cfg.AS.groups)`'
 output:
  html_document
---as a result of parsing YAML header from /nas/weka.gel.zone/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/Scripts/AberrantSplicing/pipeline/FRASER/Datasets.R.

Parsed params: {'title': 'Full FRASER analysis over all datasets', 'wb': {'log': [{'snakemake': '`sm str(tmp_dir / "AS" / "FRASER_datasets.Rds")`'}], 'input': [{'fraser_summary': '`sm expand(config["htmlOutputPath"] + "/AberrantSplicing/{dataset}--{annotation}_summary.html", annotation=cfg.genome.getGeneVersions(), dataset=cfg.AS.groups)`'}]}, 'output': 'html_document'}
.
Got ---
 title: "FRASER Summary: `r paste(snakemake@wildcards$dataset, snakemake@wildcards$annotation, sep = '--')`"
 author: mumichae, vyepez, ischeller
 wb:
  log:
    - snakemake: '`sm str(tmp_dir / "AS" / "{dataset}--{annotation}" / "FRASER_summary.Rds")`'
  params:
   - setup: '`sm cfg.AS.getWorkdir() + "/config.R"`'
  input:
   - fdsin: '`sm cfg.getProcessedResultsDir() +
                 "/aberrant_splicing/datasets/savedObjects/{dataset}--{annotation}/fds-object.RDS"`'
   - results: '`sm cfg.getProcessedResultsDir() +
                   "/aberrant_splicing/results/{annotation}/fraser/{dataset}/results.tsv"`'
  output:
   - wBhtml: '`sm config["htmlOutputPath"] +
               "/AberrantSplicing/{dataset}--{annotation}_summary.html"`'
   - res_html: '`sm config["htmlOutputPath"] +
               "/AberrantSplicing/FRASER_results_{dataset}--{annotation}.tsv"`'
  type: noindex
---as a result of parsing YAML header from /nas/weka.gel.zone/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/Scripts/AberrantSplicing/pipeline/FRASER/Summary.R.

Parsed params: {'title': "FRASER Summary: `r paste(snakemake@wildcards$dataset, snakemake@wildcards$annotation, sep = '--')`", 'author': 'mumichae, vyepez, ischeller', 'wb': {'log': [{'snakemake': '`sm str(tmp_dir / "AS" / "{dataset}--{annotation}" / "FRASER_summary.Rds")`'}], 'params': [{'setup': '`sm cfg.AS.getWorkdir() + "/config.R"`'}], 'input': [{'fdsin': '`sm cfg.getProcessedResultsDir() + "/aberrant_splicing/datasets/savedObjects/{dataset}--{annotation}/fds-object.RDS"`'}, {'results': '`sm cfg.getProcessedResultsDir() + "/aberrant_splicing/results/{annotation}/fraser/{dataset}/results.tsv"`'}], 'output': [{'wBhtml': '`sm config["htmlOutputPath"] + "/AberrantSplicing/{dataset}--{annotation}_summary.html"`'}, {'res_html': '`sm config["htmlOutputPath"] + "/AberrantSplicing/FRASER_results_{dataset}--{annotation}.tsv"`'}], 'type': 'noindex'}}
.
Parsed informations from R files: [{'file': '/nas/weka.gel.zone/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/Scripts/AberrantSplicing/pipeline/Counting/00_define_datasets_from_anno.R', 'outputFile': '/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/htmlOutput/Scripts_AberrantSplicing_pipeline_Counting_00_define_datasets_from_anno.html', 'param': {'title': 'Create datasets from annotation file', 'author': 'Christian Mertes, mumichae', 'wb': {'log': [{'snakemake': '`sm str(tmp_dir / "AS" / "{dataset}" / "00_defineDataset.Rds")`'}], 'params': [{'setup': '`sm cfg.AS.getWorkdir() + "/config.R"`'}, {'ids': '`sm lambda w: sa.getIDsByGroup(w.dataset, assay="RNA")`'}, {'fileMappingFile': '`sm cfg.getRoot() + "/file_mapping.csv"`'}], 'input': [{'sampleAnnoFile': '`sm config["sampleAnnotation"]`'}], 'output': [{'colData': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/annotations/{dataset}.tsv"`'}, {'wBhtml': '`sm config["htmlOutputPath"] + "/AberrantSplicing/annotations/{dataset}.html"`'}], 'type': 'noindex'}, 'output': {'html_document': {'code_folding': 'hide', 'code_download': True}}}}, {'file': '/nas/weka.gel.zone/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/Scripts/AberrantSplicing/pipeline/Counting/01_0_countRNA_init.R', 'outputFile': '/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/htmlOutput/Scripts_AberrantSplicing_pipeline_Counting_01_0_countRNA_init.html', 'param': {'title': 'Initialize Counting', 'author': 'Luise Schuller', 'wb': {'log': [{'snakemake': '`sm str(tmp_dir / "AS" / "{dataset}" / "01_0_init.Rds")`'}], 'params': [{'setup': '`sm cfg.AS.getWorkdir() + "/config.R"`'}, {'workingDir': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/"`'}], 'input': [{'colData': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/annotations/{dataset}.tsv"`'}], 'output': [{'fdsobj': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/savedObjects/raw-local-{dataset}/fds-object.RDS"`'}, {'done_fds': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/cache/raw-local-{dataset}/fds.done" `'}], 'type': 'script'}}}, {'file': '/nas/weka.gel.zone/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/Scripts/AberrantSplicing/pipeline/Counting/01_1_countRNA_splitReads_samplewise.R', 'outputFile': '/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/htmlOutput/Scripts_AberrantSplicing_pipeline_Counting_01_1_countRNA_splitReads_samplewise.html', 'param': {'title': 'Count Split Reads', 'author': 'Luise Schuller', 'wb': {'log': [{'snakemake': '`sm str(tmp_dir / "AS" / "{dataset}" / "splitReads" / "{sample_id}.Rds")`'}], 'params': [{'setup': '`sm cfg.AS.getWorkdir() + "/config.R"`'}, {'workingDir': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/"`'}], 'input': [{'done_fds': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/cache/raw-local-{dataset}/fds.done"`'}], 'output': [{'done_sample_splitCounts': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/cache/raw-local-{dataset}" +"/sample_tmp/splitCounts/sample_{sample_id}.done"`'}], 'threads': 3, 'type': 'script'}}}, {'file': '/nas/weka.gel.zone/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/Scripts/AberrantSplicing/pipeline/Counting/01_2_countRNA_splitReads_merge.R', 'outputFile': '/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/htmlOutput/Scripts_AberrantSplicing_pipeline_Counting_01_2_countRNA_splitReads_merge.html', 'param': {'title': 'Merge Split Counts', 'author': 'Luise Schuller', 'wb': {'log': [{'snakemake': '`sm str(tmp_dir / "AS" / "{dataset}" / "01_2_splitReadsMerge.Rds")`'}], 'params': [{'setup': '`sm cfg.AS.getWorkdir() + "/config.R"`'}, {'workingDir': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets"`'}], 'threads': 20, 'input': [{'sample_counts': '`sm lambda w: cfg.AS.getSplitCountFiles(w.dataset)`'}], 'output': [{'countsJ': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/savedObjects/raw-local-{dataset}/rawCountsJ.h5"`'}, {'gRangesSplitCounts': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/cache/raw-local-{dataset}/gRanges_splitCounts.rds"`'}, {'gRangesNonSplitCounts': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/cache/raw-local-{dataset}/gRanges_NonSplitCounts.rds"`'}, {'spliceSites': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/cache/raw-local-{dataset}/spliceSites_splitCounts.rds"`'}], 'type': 'script'}}}, {'file': '/nas/weka.gel.zone/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/Scripts/AberrantSplicing/pipeline/Counting/01_3_countRNA_nonSplitReads_samplewise.R', 'outputFile': '/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/htmlOutput/Scripts_AberrantSplicing_pipeline_Counting_01_3_countRNA_nonSplitReads_samplewise.html', 'param': {'title': 'Nonsplit Counts', 'author': 'Luise Schuller', 'wb': {'log': [{'snakemake': '`sm str(tmp_dir / "AS" / "{dataset}" / "nonsplitReads" / "{sample_id}.Rds")`'}], 'params': [{'setup': '`sm cfg.AS.getWorkdir() + "/config.R"`'}, {'workingDir': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets"`'}], 'input': [{'spliceSites': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/cache/raw-local-{dataset}/spliceSites_splitCounts.rds"`'}], 'output': [{'done_sample_nonSplitCounts': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/cache/raw-local-{dataset}/sample_tmp/nonSplitCounts/sample_{sample_id}.done"`'}], 'threads': 3, 'type': 'script'}}}, {'file': '/nas/weka.gel.zone/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/Scripts/AberrantSplicing/pipeline/Counting/01_4_countRNA_nonSplitReads_merge.R', 'outputFile': '/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/htmlOutput/Scripts_AberrantSplicing_pipeline_Counting_01_4_countRNA_nonSplitReads_merge.html', 'param': {'title': 'Merge Nonsplit Counts', 'author': 'Luise Schuller', 'wb': {'log': [{'snakemake': '`sm str(tmp_dir / "AS" / "{dataset}" / "01_4_nonSplitReadsMerge.Rds")`'}], 'params': [{'setup': '`sm cfg.AS.getWorkdir() + "/config.R"`'}, {'workingDir': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets"`'}], 'threads': 20, 'input': [{'sample_counts': '`sm lambda w: cfg.AS.getNonSplitCountFiles(w.dataset)`'}, {'gRangesNonSplitCounts': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/cache/raw-local-{dataset}/gRanges_NonSplitCounts.rds"`'}], 'output': [{'done': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/savedObjects/raw-local-{dataset}/merge_theta.done"`'}], 'type': 'script'}}}, {'file': '/nas/weka.gel.zone/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/Scripts/AberrantSplicing/pipeline/Counting/01_5_countRNA_collect.R', 'outputFile': '/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/htmlOutput/Scripts_AberrantSplicing_pipeline_Counting_01_5_countRNA_collect.html', 'param': {'title': 'Collect all counts to FRASER Object', 'author': 'Luise Schuller', 'wb': {'log': [{'snakemake': '`sm str(tmp_dir / "AS" / "{dataset}" / "01_5_collect.Rds")`'}], 'params': [{'setup': '`sm cfg.AS.getWorkdir() + "/config.R"`'}, {'workingDir': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets"`'}], 'input': [{'countsSSdone': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/savedObjects/raw-local-{dataset}/merge_theta.done"`'}, {'gRangesSplitCounts': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/cache/raw-local-{dataset}/gRanges_splitCounts.rds"`'}, {'spliceSites': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/cache/raw-local-{dataset}/spliceSites_splitCounts.rds"`'}], 'output': [{'counting_done': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/savedObjects/raw-local-{dataset}/counting.done" `'}], 'type': 'script'}}}, {'file': '/nas/weka.gel.zone/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/Scripts/AberrantSplicing/pipeline/Counting/02_psi_value_calculation_FraseR.R', 'outputFile': '/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/htmlOutput/Scripts_AberrantSplicing_pipeline_Counting_02_psi_value_calculation_FraseR.html', 'param': {'title': 'Calculate PSI values', 'author': 'Christian Mertes', 'wb': {'log': [{'snakemake': '`sm str(tmp_dir / "AS" / "{dataset}" / "02_PSIcalc.Rds")`'}], 'params': [{'setup': '`sm cfg.AS.getWorkdir() + "/config.R"`'}, {'workingDir': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/"`'}], 'threads': 30, 'input': [{'counting_done': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/savedObjects/raw-local-{dataset}/counting.done" `'}], 'output': [{'theta': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/savedObjects/raw-local-{dataset}/theta.h5"`'}], 'type': 'script'}}}, {'file': '/nas/weka.gel.zone/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/Scripts/AberrantSplicing/pipeline/Counting/03_filter_expression_FraseR.R', 'outputFile': '/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/htmlOutput/Scripts_AberrantSplicing_pipeline_Counting_03_filter_expression_FraseR.html', 'param': {'title': 'Filter and clean dataset', 'author': 'Christian Mertes', 'wb': {'log': [{'snakemake': '`sm str(tmp_dir / "AS" / "{dataset}" / "03_filter.Rds")`'}], 'params': [{'setup': '`sm cfg.AS.getWorkdir() + "/config.R"`'}, {'workingDir': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/"`'}, {'exCountIDs': '`sm lambda w: sa.getIDsByGroup(w.dataset, assay="SPLICE_COUNT")`'}], 'input': [{'theta': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/savedObjects/raw-local-{dataset}/theta.h5"`'}, {'exCounts': '`sm lambda w: cfg.AS.getExternalCounts(w.dataset, "k_j_counts")`'}], 'output': [{'fds': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/savedObjects/{dataset}/fds-object.RDS"`'}, {'done': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/savedObjects/{dataset}/filter.done" `'}], 'threads': 3, 'type': 'script'}}}, {'file': '/nas/weka.gel.zone/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/Scripts/AberrantSplicing/pipeline/Counting/DatasetsF.R', 'outputFile': '/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/htmlOutput/Scripts_AberrantSplicing_pipeline_Counting_DatasetsF.html', 'param': {'title': 'FRASER counting analysis over all datasets', 'wb': {'log': [{'snakemake': '`sm str(tmp_dir / "AS" / "CountingOverview.Rds")`'}], 'input': [{'counting_summary': '`sm expand(config["htmlOutputPath"] + "/AberrantSplicing/{dataset}_countSummary.html", dataset=cfg.AS.groups)`'}]}, 'output': 'html_document'}}, {'file': '/nas/weka.gel.zone/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/Scripts/AberrantSplicing/pipeline/Counting/Summary.R', 'outputFile': '/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/htmlOutput/Scripts_AberrantSplicing_pipeline_Counting_Summary.html', 'param': {'title': "Count Summary: `r gsub('_', ' ', snakemake@wildcards$dataset)`", 'author': 'Christian Mertes', 'wb': {'log': [{'snakemake': '`sm str(tmp_dir / "AS" / "{dataset}" / "CountSummary.Rds")`'}], 'params': [{'setup': '`sm cfg.AS.getWorkdir() + "/config.R"`'}, {'workingDir': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/"`'}], 'input': [{'filter': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/savedObjects/{dataset}/filter.done" `'}], 'output': [{'wBhtml': '`sm config["htmlOutputPath"] + "/AberrantSplicing/{dataset}_countSummary.html"`'}], 'type': 'noindex'}}}, {'file': '/nas/weka.gel.zone/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/Scripts/AberrantSplicing/pipeline/Counting/exportCounts.R', 'outputFile': '/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/htmlOutput/Scripts_AberrantSplicing_pipeline_Counting_exportCounts.html', 'param': {'title': 'Collect all counts from FRASER Object', 'author': 'mumichae, vyepez, c-mertes', 'wb': {'log': [{'snakemake': '`sm str(tmp_dir / "AS" / "{dataset}" / "{genomeAssembly}--{annotation}_export.Rds")`'}], 'params': [{'setup': '`sm cfg.AS.getWorkdir() + "/config.R"`'}], 'input': [{'annotation': '`sm cfg.getProcessedDataDir() + "/preprocess/{annotation}/txdb.db"`'}, {'fds_theta': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/savedObjects/raw-local-{dataset}/theta.h5"`'}], 'output': [{'k_counts': '`sm expand(cfg.exportCounts.getFilePattern(str_=True, expandStr=True) + "/k_{metric}_counts.tsv.gz", metric=["j", "theta"])`'}, {'n_counts': '`sm expand(cfg.exportCounts.getFilePattern(str_=True, expandStr=True) + "/n_{metric}_counts.tsv.gz", metric=["psi5", "psi3", "theta"])`'}], 'type': 'script'}}}, {'file': '/nas/weka.gel.zone/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/Scripts/AberrantSplicing/pipeline/FRASER/04_fit_hyperparameters_FraseR.R', 'outputFile': '/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/htmlOutput/Scripts_AberrantSplicing_pipeline_FRASER_04_fit_hyperparameters_FraseR.html', 'param': {'title': 'Hyper parameter optimization', 'author': 'Christian Mertes', 'wb': {'log': [{'snakemake': '`sm str(tmp_dir / "AS" / "{dataset}" / "04_hyper.Rds")`'}], 'params': [{'setup': '`sm cfg.AS.getWorkdir() + "/config.R"`'}, {'workingDir': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/"`'}], 'threads': 12, 'input': [{'filter': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/savedObjects/{dataset}/filter.done" `'}], 'output': [{'hyper': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/savedObjects/{dataset}/hyper.done" `'}], 'type': 'script'}}}, {'file': '/nas/weka.gel.zone/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/Scripts/AberrantSplicing/pipeline/FRASER/05_fit_autoencoder_FraseR.R', 'outputFile': '/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/htmlOutput/Scripts_AberrantSplicing_pipeline_FRASER_05_fit_autoencoder_FraseR.html', 'param': {'title': 'Fitting the autoencoder', 'author': 'Christian Mertes', 'wb': {'log': [{'snakemake': '`sm str(tmp_dir / "AS" / "{dataset}" / "05_fit.Rds")`'}], 'params': [{'setup': '`sm cfg.AS.getWorkdir() + "/config.R"`'}, {'workingDir': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/"`'}], 'threads': 20, 'input': [{'hyper': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/savedObjects/{dataset}/hyper.done" `'}], 'output': [{'fdsout': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/savedObjects/{dataset}/predictedMeans_theta.h5"`'}], 'type': 'script'}}}, {'file': '/nas/weka.gel.zone/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/Scripts/AberrantSplicing/pipeline/FRASER/06_calculation_stats_AE_FraseR.R', 'outputFile': '/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/htmlOutput/Scripts_AberrantSplicing_pipeline_FRASER_06_calculation_stats_AE_FraseR.html', 'param': {'title': 'Calculate P values', 'author': 'Christian Mertes', 'wb': {'log': [{'snakemake': '`sm str(tmp_dir / "AS" / "{dataset}" / "06_stats.Rds")`'}], 'params': [{'setup': '`sm cfg.AS.getWorkdir() + "/config.R"`'}, {'workingDir': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/"`'}], 'threads': 20, 'input': [{'fdsin': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/savedObjects/{dataset}/" + "predictedMeans_theta.h5"`'}], 'output': [{'fdsout': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/savedObjects/{dataset}/" + "padjBetaBinomial_theta.h5"`'}], 'type': 'script'}}}, {'file': '/nas/weka.gel.zone/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/Scripts/AberrantSplicing/pipeline/FRASER/07_extract_results_FraseR.R', 'outputFile': '/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/htmlOutput/Scripts_AberrantSplicing_pipeline_FRASER_07_extract_results_FraseR.html', 'param': {'title': 'Results of FRASER analysis', 'author': 'Christian Mertes', 'wb': {'log': [{'snakemake': '`sm str(tmp_dir / "AS" / "{dataset}--{annotation}" / "07_results.Rds")`'}], 'params': [{'workingDir': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/"`'}, {'outputDir': '`sm cfg.getProcessedResultsDir() + "/aberrant_splicing/datasets/"`'}, {'padjCutoff': '`sm cfg.AS.get("padjCutoff")`'}, {'zScoreCutoff': '`sm cfg.AS.get("zScoreCutoff")`'}, {'deltaPsiCutoff': '`sm cfg.AS.get("deltaPsiCutoff")`'}, {'hpoFile': '`sm cfg.get("hpoFile")`'}], 'threads': 10, 'input': [{'setup': '`sm cfg.AS.getWorkdir() + "/config.R"`'}, {'add_HPO_cols': '`sm str(projectDir / ".drop" / "helpers" / "add_HPO_cols.R")`'}, {'fdsin': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/savedObjects/{dataset}/" + "padjBetaBinomial_theta.h5"`'}, {'txdb': '`sm cfg.getProcessedDataDir() + "/preprocess/{annotation}/txdb.db"`'}, {'gene_name_mapping': '`sm cfg.getProcessedDataDir() + "/preprocess/{annotation}/gene_name_mapping_{annotation}.tsv"`'}], 'output': [{'resultTableJunc': '`sm cfg.getProcessedResultsDir() + "/aberrant_splicing/results/{annotation}/fraser/{dataset}/results_per_junction.tsv"`'}, {'resultTableGene': '`sm cfg.getProcessedResultsDir() + "/aberrant_splicing/results/{annotation}/fraser/{dataset}/results.tsv"`'}, {'fds': '`sm cfg.getProcessedResultsDir() + "/aberrant_splicing/datasets/savedObjects/{dataset}--{annotation}/fds-object.RDS"`'}], 'type': 'script'}}}, {'file': '/nas/weka.gel.zone/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/Scripts/AberrantSplicing/pipeline/FRASER/Datasets.R', 'outputFile': '/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/htmlOutput/Scripts_AberrantSplicing_pipeline_FRASER_Datasets.html', 'param': {'title': 'Full FRASER analysis over all datasets', 'wb': {'log': [{'snakemake': '`sm str(tmp_dir / "AS" / "FRASER_datasets.Rds")`'}], 'input': [{'fraser_summary': '`sm expand(config["htmlOutputPath"] + "/AberrantSplicing/{dataset}--{annotation}_summary.html", annotation=cfg.genome.getGeneVersions(), dataset=cfg.AS.groups)`'}]}, 'output': 'html_document'}}, {'file': '/nas/weka.gel.zone/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/Scripts/AberrantSplicing/pipeline/FRASER/Summary.R', 'outputFile': '/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/htmlOutput/Scripts_AberrantSplicing_pipeline_FRASER_Summary.html', 'param': {'title': "FRASER Summary: `r paste(snakemake@wildcards$dataset, snakemake@wildcards$annotation, sep = '--')`", 'author': 'mumichae, vyepez, ischeller', 'wb': {'log': [{'snakemake': '`sm str(tmp_dir / "AS" / "{dataset}--{annotation}" / "FRASER_summary.Rds")`'}], 'params': [{'setup': '`sm cfg.AS.getWorkdir() + "/config.R"`'}], 'input': [{'fdsin': '`sm cfg.getProcessedResultsDir() + "/aberrant_splicing/datasets/savedObjects/{dataset}--{annotation}/fds-object.RDS"`'}, {'results': '`sm cfg.getProcessedResultsDir() + "/aberrant_splicing/results/{annotation}/fraser/{dataset}/results.tsv"`'}], 'output': [{'wBhtml': '`sm config["htmlOutputPath"] + "/AberrantSplicing/{dataset}--{annotation}_summary.html"`'}, {'res_html': '`sm config["htmlOutputPath"] + "/AberrantSplicing/FRASER_results_{dataset}--{annotation}.tsv"`'}], 'type': 'noindex'}}}]
Finding .md files:

Found files in scope of wBuild: ['/nas/weka.gel.zone/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/Scripts/AberrantSplicing/pipeline/aberrant_splicing_readme.md'].

Found /pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/htmlOutput/Scripts_AberrantSplicing_pipeline_aberrant_splicing_readme.html.

MonoallelicExpression has been turned off in the config file
rnaVariantCalling has been turned off in the config file
Structuring dependencies...
Loaded config.
 html output path (key htmlOutputPath): /pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/htmlOutput

Found files in scope of wBuild: ['Scripts/AberrantSplicing/Overview.R', 'Scripts/AberrantSplicing/pipeline/Counting/00_define_datasets_from_anno.R', 'Scripts/AberrantSplicing/pipeline/Counting/01_0_countRNA_init.R', 'Scripts/AberrantSplicing/pipeline/Counting/01_1_countRNA_splitReads_samplewise.R', 'Scripts/AberrantSplicing/pipeline/Counting/01_2_countRNA_splitReads_merge.R', 'Scripts/AberrantSplicing/pipeline/Counting/01_3_countRNA_nonSplitReads_samplewise.R', 'Scripts/AberrantSplicing/pipeline/Counting/01_4_countRNA_nonSplitReads_merge.R', 'Scripts/AberrantSplicing/pipeline/Counting/01_5_countRNA_collect.R', 'Scripts/AberrantSplicing/pipeline/Counting/02_psi_value_calculation_FraseR.R', 'Scripts/AberrantSplicing/pipeline/Counting/03_filter_expression_FraseR.R', 'Scripts/AberrantSplicing/pipeline/Counting/DatasetsF.R', 'Scripts/AberrantSplicing/pipeline/Counting/Summary.R', 'Scripts/AberrantSplicing/pipeline/Counting/exportCounts.R', 'Scripts/AberrantSplicing/pipeline/FRASER/04_fit_hyperparameters_FraseR.R', 'Scripts/AberrantSplicing/pipeline/FRASER/05_fit_autoencoder_FraseR.R', 'Scripts/AberrantSplicing/pipeline/FRASER/06_calculation_stats_AE_FraseR.R', 'Scripts/AberrantSplicing/pipeline/FRASER/07_extract_results_FraseR.R', 'Scripts/AberrantSplicing/pipeline/FRASER/Datasets.R', 'Scripts/AberrantSplicing/pipeline/FRASER/Summary.R', 'Scripts/AberrantSplicing/pipeline/config.R', 'Scripts/Pipeline/SampleAnnotation.R', 'Scripts/Pipeline/preprocessGeneAnnotation.R', 'Scripts/html_functions.R'].

Got ---
 title: Aberrant Splicing
 author:
 wb:
  log:
    - snakemake: '`sm str(tmp_dir / "AS" / "Overview.Rds")`'
  params:
    - annotations: '`sm cfg.genome.getGeneVersions()`'
    - datasets: '`sm cfg.AS.groups`'
    - htmlDir: '`sm config["htmlOutputPath"] + "/AberrantSplicing"`'
  input:
    - functions: '`sm cfg.workDir / "Scripts/html_functions.R"`'
    - fds_files: '`sm expand(cfg.getProcessedResultsDir() +
                "/aberrant_splicing/datasets/savedObjects/{dataset}--{annotation}/" +
                "fds-object.RDS", dataset=cfg.AS.groups, annotation=cfg.genome.getGeneVersions())`'
    - result_tables: '`sm expand(cfg.getProcessedResultsDir() +
                    "/aberrant_splicing/results/{annotation}/fraser/{dataset}/results_per_junction.tsv",
                    dataset=cfg.AS.groups, annotation=cfg.genome.getGeneVersions())`'
 output:
   html_document:
    code_folding: show
    code_download: TRUE
---as a result of parsing YAML header from Scripts/AberrantSplicing/Overview.R.

Parsed params: {'title': 'Aberrant Splicing', 'author': None, 'wb': {'log': [{'snakemake': '`sm str(tmp_dir / "AS" / "Overview.Rds")`'}], 'params': [{'annotations': '`sm cfg.genome.getGeneVersions()`'}, {'datasets': '`sm cfg.AS.groups`'}, {'htmlDir': '`sm config["htmlOutputPath"] + "/AberrantSplicing"`'}], 'input': [{'functions': '`sm cfg.workDir / "Scripts/html_functions.R"`'}, {'fds_files': '`sm expand(cfg.getProcessedResultsDir() + "/aberrant_splicing/datasets/savedObjects/{dataset}--{annotation}/" + "fds-object.RDS", dataset=cfg.AS.groups, annotation=cfg.genome.getGeneVersions())`'}, {'result_tables': '`sm expand(cfg.getProcessedResultsDir() + "/aberrant_splicing/results/{annotation}/fraser/{dataset}/results_per_junction.tsv", dataset=cfg.AS.groups, annotation=cfg.genome.getGeneVersions())`'}]}, 'output': {'html_document': {'code_folding': 'show', 'code_download': True}}}
.
Got ---
 title: Create datasets from annotation file
 author: Christian Mertes, mumichae
 wb:
  log:
    - snakemake: '`sm str(tmp_dir / "AS" / "{dataset}" / "00_defineDataset.Rds")`'
  params:
    - setup: '`sm cfg.AS.getWorkdir() + "/config.R"`'
    - ids: '`sm lambda w: sa.getIDsByGroup(w.dataset, assay="RNA")`'
    - fileMappingFile: '`sm cfg.getRoot() + "/file_mapping.csv"`'
  input:
    - sampleAnnoFile: '`sm config["sampleAnnotation"]`'
  output:
    - colData: '`sm cfg.getProcessedDataDir() +
                    "/aberrant_splicing/annotations/{dataset}.tsv"`'
    - wBhtml:  '`sm config["htmlOutputPath"] +
                    "/AberrantSplicing/annotations/{dataset}.html"`'
  type: noindex
 output:
  html_document:
   code_folding: hide
   code_download: TRUE
---as a result of parsing YAML header from Scripts/AberrantSplicing/pipeline/Counting/00_define_datasets_from_anno.R.

Parsed params: {'title': 'Create datasets from annotation file', 'author': 'Christian Mertes, mumichae', 'wb': {'log': [{'snakemake': '`sm str(tmp_dir / "AS" / "{dataset}" / "00_defineDataset.Rds")`'}], 'params': [{'setup': '`sm cfg.AS.getWorkdir() + "/config.R"`'}, {'ids': '`sm lambda w: sa.getIDsByGroup(w.dataset, assay="RNA")`'}, {'fileMappingFile': '`sm cfg.getRoot() + "/file_mapping.csv"`'}], 'input': [{'sampleAnnoFile': '`sm config["sampleAnnotation"]`'}], 'output': [{'colData': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/annotations/{dataset}.tsv"`'}, {'wBhtml': '`sm config["htmlOutputPath"] + "/AberrantSplicing/annotations/{dataset}.html"`'}], 'type': 'noindex'}, 'output': {'html_document': {'code_folding': 'hide', 'code_download': True}}}
.
Got ---
 title: Initialize Counting
 author: Luise Schuller
 wb:
  log:
    - snakemake: '`sm str(tmp_dir / "AS" / "{dataset}" / "01_0_init.Rds")`'
  params:
   - setup: '`sm cfg.AS.getWorkdir() + "/config.R"`'
   - workingDir: '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/"`'
  input:
    - colData: '`sm cfg.getProcessedDataDir() +
                    "/aberrant_splicing/annotations/{dataset}.tsv"`'
  output:
   - fdsobj:  '`sm cfg.getProcessedDataDir() +
                   "/aberrant_splicing/datasets/savedObjects/raw-local-{dataset}/fds-object.RDS"`'
   - done_fds: '`sm cfg.getProcessedDataDir() +
                "/aberrant_splicing/datasets/cache/raw-local-{dataset}/fds.done" `'
  type: script
---as a result of parsing YAML header from Scripts/AberrantSplicing/pipeline/Counting/01_0_countRNA_init.R.

Parsed params: {'title': 'Initialize Counting', 'author': 'Luise Schuller', 'wb': {'log': [{'snakemake': '`sm str(tmp_dir / "AS" / "{dataset}" / "01_0_init.Rds")`'}], 'params': [{'setup': '`sm cfg.AS.getWorkdir() + "/config.R"`'}, {'workingDir': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/"`'}], 'input': [{'colData': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/annotations/{dataset}.tsv"`'}], 'output': [{'fdsobj': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/savedObjects/raw-local-{dataset}/fds-object.RDS"`'}, {'done_fds': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/cache/raw-local-{dataset}/fds.done" `'}], 'type': 'script'}}
.
Got ---
 title: Count Split Reads
 author: Luise Schuller
 wb:
  log:
    - snakemake: '`sm str(tmp_dir / "AS" / "{dataset}" / "splitReads" / "{sample_id}.Rds")`'
  params:
   - setup: '`sm cfg.AS.getWorkdir() + "/config.R"`'
   - workingDir: '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/"`'
  input:
   - done_fds: '`sm cfg.getProcessedDataDir() +
                "/aberrant_splicing/datasets/cache/raw-local-{dataset}/fds.done"`'
  output:
   - done_sample_splitCounts: '`sm cfg.getProcessedDataDir() +
                "/aberrant_splicing/datasets/cache/raw-local-{dataset}"
                +"/sample_tmp/splitCounts/sample_{sample_id}.done"`'
  threads: 3
  type: script
---as a result of parsing YAML header from Scripts/AberrantSplicing/pipeline/Counting/01_1_countRNA_splitReads_samplewise.R.

Parsed params: {'title': 'Count Split Reads', 'author': 'Luise Schuller', 'wb': {'log': [{'snakemake': '`sm str(tmp_dir / "AS" / "{dataset}" / "splitReads" / "{sample_id}.Rds")`'}], 'params': [{'setup': '`sm cfg.AS.getWorkdir() + "/config.R"`'}, {'workingDir': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/"`'}], 'input': [{'done_fds': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/cache/raw-local-{dataset}/fds.done"`'}], 'output': [{'done_sample_splitCounts': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/cache/raw-local-{dataset}" +"/sample_tmp/splitCounts/sample_{sample_id}.done"`'}], 'threads': 3, 'type': 'script'}}
.
Got ---
 title: Merge Split Counts
 author: Luise Schuller
 wb:
  log:
    - snakemake: '`sm str(tmp_dir / "AS" / "{dataset}" / "01_2_splitReadsMerge.Rds")`'
  params:
   - setup: '`sm cfg.AS.getWorkdir() + "/config.R"`'
   - workingDir: '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets"`'
  threads: 20
  input:
   - sample_counts: '`sm lambda w: cfg.AS.getSplitCountFiles(w.dataset)`'
  output:
   - countsJ: '`sm cfg.getProcessedDataDir() +
                          "/aberrant_splicing/datasets/savedObjects/raw-local-{dataset}/rawCountsJ.h5"`'
   - gRangesSplitCounts: '`sm cfg.getProcessedDataDir() +
                          "/aberrant_splicing/datasets/cache/raw-local-{dataset}/gRanges_splitCounts.rds"`'
   - gRangesNonSplitCounts: '`sm cfg.getProcessedDataDir() +
                          "/aberrant_splicing/datasets/cache/raw-local-{dataset}/gRanges_NonSplitCounts.rds"`'
   - spliceSites: '`sm cfg.getProcessedDataDir() +
                   "/aberrant_splicing/datasets/cache/raw-local-{dataset}/spliceSites_splitCounts.rds"`'
  type: script
---as a result of parsing YAML header from Scripts/AberrantSplicing/pipeline/Counting/01_2_countRNA_splitReads_merge.R.

Parsed params: {'title': 'Merge Split Counts', 'author': 'Luise Schuller', 'wb': {'log': [{'snakemake': '`sm str(tmp_dir / "AS" / "{dataset}" / "01_2_splitReadsMerge.Rds")`'}], 'params': [{'setup': '`sm cfg.AS.getWorkdir() + "/config.R"`'}, {'workingDir': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets"`'}], 'threads': 20, 'input': [{'sample_counts': '`sm lambda w: cfg.AS.getSplitCountFiles(w.dataset)`'}], 'output': [{'countsJ': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/savedObjects/raw-local-{dataset}/rawCountsJ.h5"`'}, {'gRangesSplitCounts': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/cache/raw-local-{dataset}/gRanges_splitCounts.rds"`'}, {'gRangesNonSplitCounts': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/cache/raw-local-{dataset}/gRanges_NonSplitCounts.rds"`'}, {'spliceSites': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/cache/raw-local-{dataset}/spliceSites_splitCounts.rds"`'}], 'type': 'script'}}
.
Got ---
 title: Nonsplit Counts
 author: Luise Schuller
 wb:
  log:
    - snakemake: '`sm str(tmp_dir / "AS" / "{dataset}" / "nonsplitReads" / "{sample_id}.Rds")`'
  params:
   - setup: '`sm cfg.AS.getWorkdir() + "/config.R"`'
   - workingDir: '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets"`'
  input:
   - spliceSites: '`sm cfg.getProcessedDataDir() +
                   "/aberrant_splicing/datasets/cache/raw-local-{dataset}/spliceSites_splitCounts.rds"`'
  output:
   - done_sample_nonSplitCounts : '`sm cfg.getProcessedDataDir() +
                   "/aberrant_splicing/datasets/cache/raw-local-{dataset}/sample_tmp/nonSplitCounts/sample_{sample_id}.done"`'
  threads: 3
  type: script
---as a result of parsing YAML header from Scripts/AberrantSplicing/pipeline/Counting/01_3_countRNA_nonSplitReads_samplewise.R.

Parsed params: {'title': 'Nonsplit Counts', 'author': 'Luise Schuller', 'wb': {'log': [{'snakemake': '`sm str(tmp_dir / "AS" / "{dataset}" / "nonsplitReads" / "{sample_id}.Rds")`'}], 'params': [{'setup': '`sm cfg.AS.getWorkdir() + "/config.R"`'}, {'workingDir': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets"`'}], 'input': [{'spliceSites': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/cache/raw-local-{dataset}/spliceSites_splitCounts.rds"`'}], 'output': [{'done_sample_nonSplitCounts': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/cache/raw-local-{dataset}/sample_tmp/nonSplitCounts/sample_{sample_id}.done"`'}], 'threads': 3, 'type': 'script'}}
.
Got ---
 title: Merge Nonsplit Counts
 author: Luise Schuller
 wb:
  log:
    - snakemake: '`sm str(tmp_dir / "AS" / "{dataset}" / "01_4_nonSplitReadsMerge.Rds")`'
  params:
   - setup: '`sm cfg.AS.getWorkdir() + "/config.R"`'
   - workingDir: '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets"`'
  threads: 20
  input:
   - sample_counts:  '`sm lambda w: cfg.AS.getNonSplitCountFiles(w.dataset)`'
   - gRangesNonSplitCounts: '`sm cfg.getProcessedDataDir() +
                          "/aberrant_splicing/datasets/cache/raw-local-{dataset}/gRanges_NonSplitCounts.rds"`'
  output:
#   - countsSS: '`sm cfg.getProcessedDataDir() +
#                   "/aberrant_splicing/datasets/savedObjects/raw-local-{dataset}/rawCountsSS.h5"`'
   - done:     '`sm cfg.getProcessedDataDir() +
                "/aberrant_splicing/datasets/savedObjects/raw-local-{dataset}/merge_theta.done"`'
  type: script
---as a result of parsing YAML header from Scripts/AberrantSplicing/pipeline/Counting/01_4_countRNA_nonSplitReads_merge.R.

Parsed params: {'title': 'Merge Nonsplit Counts', 'author': 'Luise Schuller', 'wb': {'log': [{'snakemake': '`sm str(tmp_dir / "AS" / "{dataset}" / "01_4_nonSplitReadsMerge.Rds")`'}], 'params': [{'setup': '`sm cfg.AS.getWorkdir() + "/config.R"`'}, {'workingDir': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets"`'}], 'threads': 20, 'input': [{'sample_counts': '`sm lambda w: cfg.AS.getNonSplitCountFiles(w.dataset)`'}, {'gRangesNonSplitCounts': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/cache/raw-local-{dataset}/gRanges_NonSplitCounts.rds"`'}], 'output': [{'done': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/savedObjects/raw-local-{dataset}/merge_theta.done"`'}], 'type': 'script'}}
.
Got ---
 title: Collect all counts to FRASER Object
 author: Luise Schuller
 wb:
  log:
    - snakemake: '`sm str(tmp_dir / "AS" / "{dataset}" / "01_5_collect.Rds")`'
  params:
   - setup: '`sm cfg.AS.getWorkdir() + "/config.R"`'
   - workingDir: '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets"`'
  input:
    - countsSSdone: '`sm cfg.getProcessedDataDir() +
                          "/aberrant_splicing/datasets/savedObjects/raw-local-{dataset}/merge_theta.done"`'
    - gRangesSplitCounts: '`sm cfg.getProcessedDataDir() +
                          "/aberrant_splicing/datasets/cache/raw-local-{dataset}/gRanges_splitCounts.rds"`'
    - spliceSites: '`sm cfg.getProcessedDataDir() +
                          "/aberrant_splicing/datasets/cache/raw-local-{dataset}/spliceSites_splitCounts.rds"`'
  output:
   - counting_done: '`sm cfg.getProcessedDataDir() +
                          "/aberrant_splicing/datasets/savedObjects/raw-local-{dataset}/counting.done" `'
  type: script
---as a result of parsing YAML header from Scripts/AberrantSplicing/pipeline/Counting/01_5_countRNA_collect.R.

Parsed params: {'title': 'Collect all counts to FRASER Object', 'author': 'Luise Schuller', 'wb': {'log': [{'snakemake': '`sm str(tmp_dir / "AS" / "{dataset}" / "01_5_collect.Rds")`'}], 'params': [{'setup': '`sm cfg.AS.getWorkdir() + "/config.R"`'}, {'workingDir': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets"`'}], 'input': [{'countsSSdone': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/savedObjects/raw-local-{dataset}/merge_theta.done"`'}, {'gRangesSplitCounts': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/cache/raw-local-{dataset}/gRanges_splitCounts.rds"`'}, {'spliceSites': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/cache/raw-local-{dataset}/spliceSites_splitCounts.rds"`'}], 'output': [{'counting_done': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/savedObjects/raw-local-{dataset}/counting.done" `'}], 'type': 'script'}}
.
Got ---
 title: Calculate PSI values
 author: Christian Mertes
 wb:
  log:
   - snakemake: '`sm str(tmp_dir / "AS" / "{dataset}" / "02_PSIcalc.Rds")`'
  params:
   - setup: '`sm cfg.AS.getWorkdir() + "/config.R"`'
   - workingDir: '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/"`'
  threads: 30
  input:
   - counting_done: '`sm cfg.getProcessedDataDir() +
                "/aberrant_splicing/datasets/savedObjects/raw-local-{dataset}/counting.done" `'
  output:
  - theta:     '`sm cfg.getProcessedDataDir() +
                    "/aberrant_splicing/datasets/savedObjects/raw-local-{dataset}/theta.h5"`'
  type: script
---as a result of parsing YAML header from Scripts/AberrantSplicing/pipeline/Counting/02_psi_value_calculation_FraseR.R.

Parsed params: {'title': 'Calculate PSI values', 'author': 'Christian Mertes', 'wb': {'log': [{'snakemake': '`sm str(tmp_dir / "AS" / "{dataset}" / "02_PSIcalc.Rds")`'}], 'params': [{'setup': '`sm cfg.AS.getWorkdir() + "/config.R"`'}, {'workingDir': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/"`'}], 'threads': 30, 'input': [{'counting_done': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/savedObjects/raw-local-{dataset}/counting.done" `'}], 'output': [{'theta': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/savedObjects/raw-local-{dataset}/theta.h5"`'}], 'type': 'script'}}
.
Got ---
 title: Filter and clean dataset
 author: Christian Mertes
 wb:
  log:
    - snakemake: '`sm str(tmp_dir / "AS" / "{dataset}" / "03_filter.Rds")`'
  params:
   - setup: '`sm cfg.AS.getWorkdir() + "/config.R"`'
   - workingDir: '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/"`'
   - exCountIDs: '`sm lambda w: sa.getIDsByGroup(w.dataset, assay="SPLICE_COUNT")`'
  input:
   - theta:  '`sm cfg.getProcessedDataDir() +
                  "/aberrant_splicing/datasets/savedObjects/raw-local-{dataset}/theta.h5"`'
   - exCounts: '`sm lambda w: cfg.AS.getExternalCounts(w.dataset, "k_j_counts")`'
  output:
   - fds: '`sm cfg.getProcessedDataDir() +
                  "/aberrant_splicing/datasets/savedObjects/{dataset}/fds-object.RDS"`'
   - done: '`sm cfg.getProcessedDataDir() +
                  "/aberrant_splicing/datasets/savedObjects/{dataset}/filter.done" `'
  threads: 3
  type: script
---as a result of parsing YAML header from Scripts/AberrantSplicing/pipeline/Counting/03_filter_expression_FraseR.R.

Parsed params: {'title': 'Filter and clean dataset', 'author': 'Christian Mertes', 'wb': {'log': [{'snakemake': '`sm str(tmp_dir / "AS" / "{dataset}" / "03_filter.Rds")`'}], 'params': [{'setup': '`sm cfg.AS.getWorkdir() + "/config.R"`'}, {'workingDir': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/"`'}, {'exCountIDs': '`sm lambda w: sa.getIDsByGroup(w.dataset, assay="SPLICE_COUNT")`'}], 'input': [{'theta': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/savedObjects/raw-local-{dataset}/theta.h5"`'}, {'exCounts': '`sm lambda w: cfg.AS.getExternalCounts(w.dataset, "k_j_counts")`'}], 'output': [{'fds': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/savedObjects/{dataset}/fds-object.RDS"`'}, {'done': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/savedObjects/{dataset}/filter.done" `'}], 'threads': 3, 'type': 'script'}}
.
Got ---
 title: FRASER counting analysis over all datasets
 wb:
  log:
    - snakemake: '`sm str(tmp_dir / "AS" / "CountingOverview.Rds")`'
  input:
   - counting_summary: '`sm expand(config["htmlOutputPath"] +
                     "/AberrantSplicing/{dataset}_countSummary.html",
                     dataset=cfg.AS.groups)`'
 output:
  html_document
---as a result of parsing YAML header from Scripts/AberrantSplicing/pipeline/Counting/DatasetsF.R.

Parsed params: {'title': 'FRASER counting analysis over all datasets', 'wb': {'log': [{'snakemake': '`sm str(tmp_dir / "AS" / "CountingOverview.Rds")`'}], 'input': [{'counting_summary': '`sm expand(config["htmlOutputPath"] + "/AberrantSplicing/{dataset}_countSummary.html", dataset=cfg.AS.groups)`'}]}, 'output': 'html_document'}
.
Got ---
 title: "Count Summary: `r gsub('_', ' ', snakemake@wildcards$dataset)`"
 author: Christian Mertes
 wb:
  log:
    - snakemake: '`sm str(tmp_dir / "AS" / "{dataset}" / "CountSummary.Rds")`'
  params:
   - setup: '`sm cfg.AS.getWorkdir() + "/config.R"`'
   - workingDir: '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/"`'
  input:
   - filter: '`sm cfg.getProcessedDataDir() +
                "/aberrant_splicing/datasets/savedObjects/{dataset}/filter.done" `'
  output:
   - wBhtml: '`sm config["htmlOutputPath"] +
                  "/AberrantSplicing/{dataset}_countSummary.html"`'
  type: noindex
---as a result of parsing YAML header from Scripts/AberrantSplicing/pipeline/Counting/Summary.R.

Parsed params: {'title': "Count Summary: `r gsub('_', ' ', snakemake@wildcards$dataset)`", 'author': 'Christian Mertes', 'wb': {'log': [{'snakemake': '`sm str(tmp_dir / "AS" / "{dataset}" / "CountSummary.Rds")`'}], 'params': [{'setup': '`sm cfg.AS.getWorkdir() + "/config.R"`'}, {'workingDir': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/"`'}], 'input': [{'filter': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/savedObjects/{dataset}/filter.done" `'}], 'output': [{'wBhtml': '`sm config["htmlOutputPath"] + "/AberrantSplicing/{dataset}_countSummary.html"`'}], 'type': 'noindex'}}
.
Got ---
 title: Collect all counts from FRASER Object
 author: mumichae, vyepez, c-mertes
 wb:
  log:
    - snakemake: '`sm str(tmp_dir / "AS" / "{dataset}" / "{genomeAssembly}--{annotation}_export.Rds")`'
  params:
   - setup: '`sm cfg.AS.getWorkdir() + "/config.R"`'

  input:
   - annotation: '`sm cfg.getProcessedDataDir() + "/preprocess/{annotation}/txdb.db"`'
   - fds_theta: '`sm cfg.getProcessedDataDir() +
                    "/aberrant_splicing/datasets/savedObjects/raw-local-{dataset}/theta.h5"`'
  output:
    - k_counts: '`sm expand(cfg.exportCounts.getFilePattern(str_=True, expandStr=True) + "/k_{metric}_counts.tsv.gz", metric=["j", "theta"])`'
    - n_counts: '`sm expand(cfg.exportCounts.getFilePattern(str_=True, expandStr=True) + "/n_{metric}_counts.tsv.gz", metric=["psi5", "psi3", "theta"])`'
  type: script
---as a result of parsing YAML header from Scripts/AberrantSplicing/pipeline/Counting/exportCounts.R.

Parsed params: {'title': 'Collect all counts from FRASER Object', 'author': 'mumichae, vyepez, c-mertes', 'wb': {'log': [{'snakemake': '`sm str(tmp_dir / "AS" / "{dataset}" / "{genomeAssembly}--{annotation}_export.Rds")`'}], 'params': [{'setup': '`sm cfg.AS.getWorkdir() + "/config.R"`'}], 'input': [{'annotation': '`sm cfg.getProcessedDataDir() + "/preprocess/{annotation}/txdb.db"`'}, {'fds_theta': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/savedObjects/raw-local-{dataset}/theta.h5"`'}], 'output': [{'k_counts': '`sm expand(cfg.exportCounts.getFilePattern(str_=True, expandStr=True) + "/k_{metric}_counts.tsv.gz", metric=["j", "theta"])`'}, {'n_counts': '`sm expand(cfg.exportCounts.getFilePattern(str_=True, expandStr=True) + "/n_{metric}_counts.tsv.gz", metric=["psi5", "psi3", "theta"])`'}], 'type': 'script'}}
.
Got ---
 title: Hyper parameter optimization
 author: Christian Mertes
 wb:
  log:
    - snakemake: '`sm str(tmp_dir / "AS" / "{dataset}" / "04_hyper.Rds")`'
  params:
   - setup: '`sm cfg.AS.getWorkdir() + "/config.R"`'
   - workingDir: '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/"`'
  threads: 12
  input:
   - filter: '`sm cfg.getProcessedDataDir() +
                "/aberrant_splicing/datasets/savedObjects/{dataset}/filter.done" `'
  output:
   - hyper: '`sm cfg.getProcessedDataDir() +
                "/aberrant_splicing/datasets/savedObjects/{dataset}/hyper.done" `'
  type: script
---as a result of parsing YAML header from Scripts/AberrantSplicing/pipeline/FRASER/04_fit_hyperparameters_FraseR.R.

Parsed params: {'title': 'Hyper parameter optimization', 'author': 'Christian Mertes', 'wb': {'log': [{'snakemake': '`sm str(tmp_dir / "AS" / "{dataset}" / "04_hyper.Rds")`'}], 'params': [{'setup': '`sm cfg.AS.getWorkdir() + "/config.R"`'}, {'workingDir': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/"`'}], 'threads': 12, 'input': [{'filter': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/savedObjects/{dataset}/filter.done" `'}], 'output': [{'hyper': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/savedObjects/{dataset}/hyper.done" `'}], 'type': 'script'}}
.
Got ---
 title: Fitting the autoencoder
 author: Christian Mertes
 wb:
  log:
    - snakemake: '`sm str(tmp_dir / "AS" / "{dataset}" / "05_fit.Rds")`'
  params:
   - setup: '`sm cfg.AS.getWorkdir() + "/config.R"`'
   - workingDir: '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/"`'
  threads: 20
  input:
   - hyper: '`sm cfg.getProcessedDataDir() +
                "/aberrant_splicing/datasets/savedObjects/{dataset}/hyper.done" `'
  output:
   - fdsout: '`sm cfg.getProcessedDataDir() +
                  "/aberrant_splicing/datasets/savedObjects/{dataset}/predictedMeans_theta.h5"`'
  type: script
---as a result of parsing YAML header from Scripts/AberrantSplicing/pipeline/FRASER/05_fit_autoencoder_FraseR.R.

Parsed params: {'title': 'Fitting the autoencoder', 'author': 'Christian Mertes', 'wb': {'log': [{'snakemake': '`sm str(tmp_dir / "AS" / "{dataset}" / "05_fit.Rds")`'}], 'params': [{'setup': '`sm cfg.AS.getWorkdir() + "/config.R"`'}, {'workingDir': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/"`'}], 'threads': 20, 'input': [{'hyper': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/savedObjects/{dataset}/hyper.done" `'}], 'output': [{'fdsout': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/savedObjects/{dataset}/predictedMeans_theta.h5"`'}], 'type': 'script'}}
.
Got ---
 title: Calculate P values
 author: Christian Mertes
 wb:
  log:
    - snakemake: '`sm str(tmp_dir / "AS" / "{dataset}" / "06_stats.Rds")`'
  params:
   - setup: '`sm cfg.AS.getWorkdir() + "/config.R"`'
   - workingDir: '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/"`'
  threads: 20
  input:
   - fdsin:  '`sm cfg.getProcessedDataDir() +
                  "/aberrant_splicing/datasets/savedObjects/{dataset}/" +
                  "predictedMeans_theta.h5"`'
  output:
   - fdsout: '`sm cfg.getProcessedDataDir() +
                  "/aberrant_splicing/datasets/savedObjects/{dataset}/" +
                  "padjBetaBinomial_theta.h5"`'
  type: script
---as a result of parsing YAML header from Scripts/AberrantSplicing/pipeline/FRASER/06_calculation_stats_AE_FraseR.R.

Parsed params: {'title': 'Calculate P values', 'author': 'Christian Mertes', 'wb': {'log': [{'snakemake': '`sm str(tmp_dir / "AS" / "{dataset}" / "06_stats.Rds")`'}], 'params': [{'setup': '`sm cfg.AS.getWorkdir() + "/config.R"`'}, {'workingDir': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/"`'}], 'threads': 20, 'input': [{'fdsin': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/savedObjects/{dataset}/" + "predictedMeans_theta.h5"`'}], 'output': [{'fdsout': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/savedObjects/{dataset}/" + "padjBetaBinomial_theta.h5"`'}], 'type': 'script'}}
.
Got ---
 title: Results of FRASER analysis
 author: Christian Mertes
 wb:
  log:
    - snakemake: '`sm str(tmp_dir / "AS" / "{dataset}--{annotation}" / "07_results.Rds")`'
  params:
   - workingDir: '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/"`'
   - outputDir: '`sm cfg.getProcessedResultsDir() + "/aberrant_splicing/datasets/"`'
   - padjCutoff: '`sm cfg.AS.get("padjCutoff")`'
   - zScoreCutoff: '`sm cfg.AS.get("zScoreCutoff")`'
   - deltaPsiCutoff: '`sm cfg.AS.get("deltaPsiCutoff")`'
   - hpoFile: '`sm cfg.get("hpoFile")`'
  threads: 10
  input:
   - setup: '`sm cfg.AS.getWorkdir() + "/config.R"`'
   - add_HPO_cols: '`sm str(projectDir / ".drop" / "helpers" / "add_HPO_cols.R")`'
   - fdsin: '`sm cfg.getProcessedDataDir() +
                 "/aberrant_splicing/datasets/savedObjects/{dataset}/" +
                 "padjBetaBinomial_theta.h5"`'
   - txdb: '`sm cfg.getProcessedDataDir() + "/preprocess/{annotation}/txdb.db"`'
   - gene_name_mapping: '`sm cfg.getProcessedDataDir() + "/preprocess/{annotation}/gene_name_mapping_{annotation}.tsv"`'
  output:
   - resultTableJunc: '`sm cfg.getProcessedResultsDir() +
                          "/aberrant_splicing/results/{annotation}/fraser/{dataset}/results_per_junction.tsv"`'
   - resultTableGene: '`sm cfg.getProcessedResultsDir() +
                          "/aberrant_splicing/results/{annotation}/fraser/{dataset}/results.tsv"`'
   - fds: '`sm cfg.getProcessedResultsDir() +
                 "/aberrant_splicing/datasets/savedObjects/{dataset}--{annotation}/fds-object.RDS"`'
  type: script
---as a result of parsing YAML header from Scripts/AberrantSplicing/pipeline/FRASER/07_extract_results_FraseR.R.

Parsed params: {'title': 'Results of FRASER analysis', 'author': 'Christian Mertes', 'wb': {'log': [{'snakemake': '`sm str(tmp_dir / "AS" / "{dataset}--{annotation}" / "07_results.Rds")`'}], 'params': [{'workingDir': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/"`'}, {'outputDir': '`sm cfg.getProcessedResultsDir() + "/aberrant_splicing/datasets/"`'}, {'padjCutoff': '`sm cfg.AS.get("padjCutoff")`'}, {'zScoreCutoff': '`sm cfg.AS.get("zScoreCutoff")`'}, {'deltaPsiCutoff': '`sm cfg.AS.get("deltaPsiCutoff")`'}, {'hpoFile': '`sm cfg.get("hpoFile")`'}], 'threads': 10, 'input': [{'setup': '`sm cfg.AS.getWorkdir() + "/config.R"`'}, {'add_HPO_cols': '`sm str(projectDir / ".drop" / "helpers" / "add_HPO_cols.R")`'}, {'fdsin': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/savedObjects/{dataset}/" + "padjBetaBinomial_theta.h5"`'}, {'txdb': '`sm cfg.getProcessedDataDir() + "/preprocess/{annotation}/txdb.db"`'}, {'gene_name_mapping': '`sm cfg.getProcessedDataDir() + "/preprocess/{annotation}/gene_name_mapping_{annotation}.tsv"`'}], 'output': [{'resultTableJunc': '`sm cfg.getProcessedResultsDir() + "/aberrant_splicing/results/{annotation}/fraser/{dataset}/results_per_junction.tsv"`'}, {'resultTableGene': '`sm cfg.getProcessedResultsDir() + "/aberrant_splicing/results/{annotation}/fraser/{dataset}/results.tsv"`'}, {'fds': '`sm cfg.getProcessedResultsDir() + "/aberrant_splicing/datasets/savedObjects/{dataset}--{annotation}/fds-object.RDS"`'}], 'type': 'script'}}
.
Got ---
 title: Full FRASER analysis over all datasets
 wb:
  log:
    - snakemake: '`sm str(tmp_dir / "AS" / "FRASER_datasets.Rds")`'
  input:
   - fraser_summary: '`sm expand(config["htmlOutputPath"] +
                     "/AberrantSplicing/{dataset}--{annotation}_summary.html",
                     annotation=cfg.genome.getGeneVersions(), dataset=cfg.AS.groups)`'
 output:
  html_document
---as a result of parsing YAML header from Scripts/AberrantSplicing/pipeline/FRASER/Datasets.R.

Parsed params: {'title': 'Full FRASER analysis over all datasets', 'wb': {'log': [{'snakemake': '`sm str(tmp_dir / "AS" / "FRASER_datasets.Rds")`'}], 'input': [{'fraser_summary': '`sm expand(config["htmlOutputPath"] + "/AberrantSplicing/{dataset}--{annotation}_summary.html", annotation=cfg.genome.getGeneVersions(), dataset=cfg.AS.groups)`'}]}, 'output': 'html_document'}
.
Got ---
 title: "FRASER Summary: `r paste(snakemake@wildcards$dataset, snakemake@wildcards$annotation, sep = '--')`"
 author: mumichae, vyepez, ischeller
 wb:
  log:
    - snakemake: '`sm str(tmp_dir / "AS" / "{dataset}--{annotation}" / "FRASER_summary.Rds")`'
  params:
   - setup: '`sm cfg.AS.getWorkdir() + "/config.R"`'
  input:
   - fdsin: '`sm cfg.getProcessedResultsDir() +
                 "/aberrant_splicing/datasets/savedObjects/{dataset}--{annotation}/fds-object.RDS"`'
   - results: '`sm cfg.getProcessedResultsDir() +
                   "/aberrant_splicing/results/{annotation}/fraser/{dataset}/results.tsv"`'
  output:
   - wBhtml: '`sm config["htmlOutputPath"] +
               "/AberrantSplicing/{dataset}--{annotation}_summary.html"`'
   - res_html: '`sm config["htmlOutputPath"] +
               "/AberrantSplicing/FRASER_results_{dataset}--{annotation}.tsv"`'
  type: noindex
---as a result of parsing YAML header from Scripts/AberrantSplicing/pipeline/FRASER/Summary.R.

Parsed params: {'title': "FRASER Summary: `r paste(snakemake@wildcards$dataset, snakemake@wildcards$annotation, sep = '--')`", 'author': 'mumichae, vyepez, ischeller', 'wb': {'log': [{'snakemake': '`sm str(tmp_dir / "AS" / "{dataset}--{annotation}" / "FRASER_summary.Rds")`'}], 'params': [{'setup': '`sm cfg.AS.getWorkdir() + "/config.R"`'}], 'input': [{'fdsin': '`sm cfg.getProcessedResultsDir() + "/aberrant_splicing/datasets/savedObjects/{dataset}--{annotation}/fds-object.RDS"`'}, {'results': '`sm cfg.getProcessedResultsDir() + "/aberrant_splicing/results/{annotation}/fraser/{dataset}/results.tsv"`'}], 'output': [{'wBhtml': '`sm config["htmlOutputPath"] + "/AberrantSplicing/{dataset}--{annotation}_summary.html"`'}, {'res_html': '`sm config["htmlOutputPath"] + "/AberrantSplicing/FRASER_results_{dataset}--{annotation}.tsv"`'}], 'type': 'noindex'}}
.
Got ---
 title: Sample Annotation Overview
 author:
 wb:
  log:
   - snakemake: '`sm str(tmp_dir / "SampleAnnotation.Rds")`'
  params:
   - hpoFile: '`sm cfg.get("hpoFile")`'
  input:
   - sampleAnnotation: '`sm sa.file`'
  output:
   - hpoOverlap: '`sm touch(cfg.getProcessedDataDir() + "/sample_anno/genes_overlapping_HPO_terms.tsv")`'
 output:
   html_document:
    code_folding: hide
    code_download: TRUE
---as a result of parsing YAML header from Scripts/Pipeline/SampleAnnotation.R.

Parsed params: {'title': 'Sample Annotation Overview', 'author': None, 'wb': {'log': [{'snakemake': '`sm str(tmp_dir / "SampleAnnotation.Rds")`'}], 'params': [{'hpoFile': '`sm cfg.get("hpoFile")`'}], 'input': [{'sampleAnnotation': '`sm sa.file`'}], 'output': [{'hpoOverlap': '`sm touch(cfg.getProcessedDataDir() + "/sample_anno/genes_overlapping_HPO_terms.tsv")`'}]}, 'output': {'html_document': {'code_folding': 'hide', 'code_download': True}}}
.
Got ---
 title: Preprocess Gene Annotations
 author: mumichae
 wb:
  log:
   - snakemake: '`sm str(tmp_dir / "AE" / "{annotation}" / "preprocess.Rds")`'
  input:
   - gtf: '`sm lambda wildcards: cfg.genome.getGeneAnnotationFile(wildcards.annotation) `'
  output:
   - txdb: '`sm cfg.getProcessedDataDir() + "/preprocess/{annotation}/txdb.db"`'
   - gene_name_mapping: '`sm cfg.getProcessedDataDir() + "/preprocess/{annotation}/gene_name_mapping_{annotation}.tsv"`'
   - count_ranges: '`sm cfg.getProcessedDataDir() +
                    "/aberrant_expression/{annotation}/count_ranges.Rds" `'
  type: script
---as a result of parsing YAML header from Scripts/Pipeline/preprocessGeneAnnotation.R.

Parsed params: {'title': 'Preprocess Gene Annotations', 'author': 'mumichae', 'wb': {'log': [{'snakemake': '`sm str(tmp_dir / "AE" / "{annotation}" / "preprocess.Rds")`'}], 'input': [{'gtf': '`sm lambda wildcards: cfg.genome.getGeneAnnotationFile(wildcards.annotation) `'}], 'output': [{'txdb': '`sm cfg.getProcessedDataDir() + "/preprocess/{annotation}/txdb.db"`'}, {'gene_name_mapping': '`sm cfg.getProcessedDataDir() + "/preprocess/{annotation}/gene_name_mapping_{annotation}.tsv"`'}, {'count_ranges': '`sm cfg.getProcessedDataDir() + "/aberrant_expression/{annotation}/count_ranges.Rds" `'}], 'type': 'script'}}
.
Parsed informations from R files: [{'file': 'Scripts/AberrantSplicing/Overview.R', 'outputFile': '/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/htmlOutput/Scripts_AberrantSplicing_Overview.html', 'param': {'title': 'Aberrant Splicing', 'author': None, 'wb': {'log': [{'snakemake': '`sm str(tmp_dir / "AS" / "Overview.Rds")`'}], 'params': [{'annotations': '`sm cfg.genome.getGeneVersions()`'}, {'datasets': '`sm cfg.AS.groups`'}, {'htmlDir': '`sm config["htmlOutputPath"] + "/AberrantSplicing"`'}], 'input': [{'functions': '`sm cfg.workDir / "Scripts/html_functions.R"`'}, {'fds_files': '`sm expand(cfg.getProcessedResultsDir() + "/aberrant_splicing/datasets/savedObjects/{dataset}--{annotation}/" + "fds-object.RDS", dataset=cfg.AS.groups, annotation=cfg.genome.getGeneVersions())`'}, {'result_tables': '`sm expand(cfg.getProcessedResultsDir() + "/aberrant_splicing/results/{annotation}/fraser/{dataset}/results_per_junction.tsv", dataset=cfg.AS.groups, annotation=cfg.genome.getGeneVersions())`'}]}, 'output': {'html_document': {'code_folding': 'show', 'code_download': True}}}}, {'file': 'Scripts/AberrantSplicing/pipeline/Counting/00_define_datasets_from_anno.R', 'outputFile': '/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/htmlOutput/Scripts_AberrantSplicing_pipeline_Counting_00_define_datasets_from_anno.html', 'param': {'title': 'Create datasets from annotation file', 'author': 'Christian Mertes, mumichae', 'wb': {'log': [{'snakemake': '`sm str(tmp_dir / "AS" / "{dataset}" / "00_defineDataset.Rds")`'}], 'params': [{'setup': '`sm cfg.AS.getWorkdir() + "/config.R"`'}, {'ids': '`sm lambda w: sa.getIDsByGroup(w.dataset, assay="RNA")`'}, {'fileMappingFile': '`sm cfg.getRoot() + "/file_mapping.csv"`'}], 'input': [{'sampleAnnoFile': '`sm config["sampleAnnotation"]`'}], 'output': [{'colData': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/annotations/{dataset}.tsv"`'}, {'wBhtml': '`sm config["htmlOutputPath"] + "/AberrantSplicing/annotations/{dataset}.html"`'}], 'type': 'noindex'}, 'output': {'html_document': {'code_folding': 'hide', 'code_download': True}}}}, {'file': 'Scripts/AberrantSplicing/pipeline/Counting/01_0_countRNA_init.R', 'outputFile': '/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/htmlOutput/Scripts_AberrantSplicing_pipeline_Counting_01_0_countRNA_init.html', 'param': {'title': 'Initialize Counting', 'author': 'Luise Schuller', 'wb': {'log': [{'snakemake': '`sm str(tmp_dir / "AS" / "{dataset}" / "01_0_init.Rds")`'}], 'params': [{'setup': '`sm cfg.AS.getWorkdir() + "/config.R"`'}, {'workingDir': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/"`'}], 'input': [{'colData': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/annotations/{dataset}.tsv"`'}], 'output': [{'fdsobj': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/savedObjects/raw-local-{dataset}/fds-object.RDS"`'}, {'done_fds': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/cache/raw-local-{dataset}/fds.done" `'}], 'type': 'script'}}}, {'file': 'Scripts/AberrantSplicing/pipeline/Counting/01_1_countRNA_splitReads_samplewise.R', 'outputFile': '/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/htmlOutput/Scripts_AberrantSplicing_pipeline_Counting_01_1_countRNA_splitReads_samplewise.html', 'param': {'title': 'Count Split Reads', 'author': 'Luise Schuller', 'wb': {'log': [{'snakemake': '`sm str(tmp_dir / "AS" / "{dataset}" / "splitReads" / "{sample_id}.Rds")`'}], 'params': [{'setup': '`sm cfg.AS.getWorkdir() + "/config.R"`'}, {'workingDir': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/"`'}], 'input': [{'done_fds': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/cache/raw-local-{dataset}/fds.done"`'}], 'output': [{'done_sample_splitCounts': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/cache/raw-local-{dataset}" +"/sample_tmp/splitCounts/sample_{sample_id}.done"`'}], 'threads': 3, 'type': 'script'}}}, {'file': 'Scripts/AberrantSplicing/pipeline/Counting/01_2_countRNA_splitReads_merge.R', 'outputFile': '/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/htmlOutput/Scripts_AberrantSplicing_pipeline_Counting_01_2_countRNA_splitReads_merge.html', 'param': {'title': 'Merge Split Counts', 'author': 'Luise Schuller', 'wb': {'log': [{'snakemake': '`sm str(tmp_dir / "AS" / "{dataset}" / "01_2_splitReadsMerge.Rds")`'}], 'params': [{'setup': '`sm cfg.AS.getWorkdir() + "/config.R"`'}, {'workingDir': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets"`'}], 'threads': 20, 'input': [{'sample_counts': '`sm lambda w: cfg.AS.getSplitCountFiles(w.dataset)`'}], 'output': [{'countsJ': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/savedObjects/raw-local-{dataset}/rawCountsJ.h5"`'}, {'gRangesSplitCounts': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/cache/raw-local-{dataset}/gRanges_splitCounts.rds"`'}, {'gRangesNonSplitCounts': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/cache/raw-local-{dataset}/gRanges_NonSplitCounts.rds"`'}, {'spliceSites': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/cache/raw-local-{dataset}/spliceSites_splitCounts.rds"`'}], 'type': 'script'}}}, {'file': 'Scripts/AberrantSplicing/pipeline/Counting/01_3_countRNA_nonSplitReads_samplewise.R', 'outputFile': '/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/htmlOutput/Scripts_AberrantSplicing_pipeline_Counting_01_3_countRNA_nonSplitReads_samplewise.html', 'param': {'title': 'Nonsplit Counts', 'author': 'Luise Schuller', 'wb': {'log': [{'snakemake': '`sm str(tmp_dir / "AS" / "{dataset}" / "nonsplitReads" / "{sample_id}.Rds")`'}], 'params': [{'setup': '`sm cfg.AS.getWorkdir() + "/config.R"`'}, {'workingDir': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets"`'}], 'input': [{'spliceSites': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/cache/raw-local-{dataset}/spliceSites_splitCounts.rds"`'}], 'output': [{'done_sample_nonSplitCounts': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/cache/raw-local-{dataset}/sample_tmp/nonSplitCounts/sample_{sample_id}.done"`'}], 'threads': 3, 'type': 'script'}}}, {'file': 'Scripts/AberrantSplicing/pipeline/Counting/01_4_countRNA_nonSplitReads_merge.R', 'outputFile': '/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/htmlOutput/Scripts_AberrantSplicing_pipeline_Counting_01_4_countRNA_nonSplitReads_merge.html', 'param': {'title': 'Merge Nonsplit Counts', 'author': 'Luise Schuller', 'wb': {'log': [{'snakemake': '`sm str(tmp_dir / "AS" / "{dataset}" / "01_4_nonSplitReadsMerge.Rds")`'}], 'params': [{'setup': '`sm cfg.AS.getWorkdir() + "/config.R"`'}, {'workingDir': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets"`'}], 'threads': 20, 'input': [{'sample_counts': '`sm lambda w: cfg.AS.getNonSplitCountFiles(w.dataset)`'}, {'gRangesNonSplitCounts': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/cache/raw-local-{dataset}/gRanges_NonSplitCounts.rds"`'}], 'output': [{'done': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/savedObjects/raw-local-{dataset}/merge_theta.done"`'}], 'type': 'script'}}}, {'file': 'Scripts/AberrantSplicing/pipeline/Counting/01_5_countRNA_collect.R', 'outputFile': '/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/htmlOutput/Scripts_AberrantSplicing_pipeline_Counting_01_5_countRNA_collect.html', 'param': {'title': 'Collect all counts to FRASER Object', 'author': 'Luise Schuller', 'wb': {'log': [{'snakemake': '`sm str(tmp_dir / "AS" / "{dataset}" / "01_5_collect.Rds")`'}], 'params': [{'setup': '`sm cfg.AS.getWorkdir() + "/config.R"`'}, {'workingDir': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets"`'}], 'input': [{'countsSSdone': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/savedObjects/raw-local-{dataset}/merge_theta.done"`'}, {'gRangesSplitCounts': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/cache/raw-local-{dataset}/gRanges_splitCounts.rds"`'}, {'spliceSites': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/cache/raw-local-{dataset}/spliceSites_splitCounts.rds"`'}], 'output': [{'counting_done': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/savedObjects/raw-local-{dataset}/counting.done" `'}], 'type': 'script'}}}, {'file': 'Scripts/AberrantSplicing/pipeline/Counting/02_psi_value_calculation_FraseR.R', 'outputFile': '/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/htmlOutput/Scripts_AberrantSplicing_pipeline_Counting_02_psi_value_calculation_FraseR.html', 'param': {'title': 'Calculate PSI values', 'author': 'Christian Mertes', 'wb': {'log': [{'snakemake': '`sm str(tmp_dir / "AS" / "{dataset}" / "02_PSIcalc.Rds")`'}], 'params': [{'setup': '`sm cfg.AS.getWorkdir() + "/config.R"`'}, {'workingDir': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/"`'}], 'threads': 30, 'input': [{'counting_done': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/savedObjects/raw-local-{dataset}/counting.done" `'}], 'output': [{'theta': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/savedObjects/raw-local-{dataset}/theta.h5"`'}], 'type': 'script'}}}, {'file': 'Scripts/AberrantSplicing/pipeline/Counting/03_filter_expression_FraseR.R', 'outputFile': '/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/htmlOutput/Scripts_AberrantSplicing_pipeline_Counting_03_filter_expression_FraseR.html', 'param': {'title': 'Filter and clean dataset', 'author': 'Christian Mertes', 'wb': {'log': [{'snakemake': '`sm str(tmp_dir / "AS" / "{dataset}" / "03_filter.Rds")`'}], 'params': [{'setup': '`sm cfg.AS.getWorkdir() + "/config.R"`'}, {'workingDir': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/"`'}, {'exCountIDs': '`sm lambda w: sa.getIDsByGroup(w.dataset, assay="SPLICE_COUNT")`'}], 'input': [{'theta': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/savedObjects/raw-local-{dataset}/theta.h5"`'}, {'exCounts': '`sm lambda w: cfg.AS.getExternalCounts(w.dataset, "k_j_counts")`'}], 'output': [{'fds': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/savedObjects/{dataset}/fds-object.RDS"`'}, {'done': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/savedObjects/{dataset}/filter.done" `'}], 'threads': 3, 'type': 'script'}}}, {'file': 'Scripts/AberrantSplicing/pipeline/Counting/DatasetsF.R', 'outputFile': '/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/htmlOutput/Scripts_AberrantSplicing_pipeline_Counting_DatasetsF.html', 'param': {'title': 'FRASER counting analysis over all datasets', 'wb': {'log': [{'snakemake': '`sm str(tmp_dir / "AS" / "CountingOverview.Rds")`'}], 'input': [{'counting_summary': '`sm expand(config["htmlOutputPath"] + "/AberrantSplicing/{dataset}_countSummary.html", dataset=cfg.AS.groups)`'}]}, 'output': 'html_document'}}, {'file': 'Scripts/AberrantSplicing/pipeline/Counting/Summary.R', 'outputFile': '/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/htmlOutput/Scripts_AberrantSplicing_pipeline_Counting_Summary.html', 'param': {'title': "Count Summary: `r gsub('_', ' ', snakemake@wildcards$dataset)`", 'author': 'Christian Mertes', 'wb': {'log': [{'snakemake': '`sm str(tmp_dir / "AS" / "{dataset}" / "CountSummary.Rds")`'}], 'params': [{'setup': '`sm cfg.AS.getWorkdir() + "/config.R"`'}, {'workingDir': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/"`'}], 'input': [{'filter': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/savedObjects/{dataset}/filter.done" `'}], 'output': [{'wBhtml': '`sm config["htmlOutputPath"] + "/AberrantSplicing/{dataset}_countSummary.html"`'}], 'type': 'noindex'}}}, {'file': 'Scripts/AberrantSplicing/pipeline/Counting/exportCounts.R', 'outputFile': '/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/htmlOutput/Scripts_AberrantSplicing_pipeline_Counting_exportCounts.html', 'param': {'title': 'Collect all counts from FRASER Object', 'author': 'mumichae, vyepez, c-mertes', 'wb': {'log': [{'snakemake': '`sm str(tmp_dir / "AS" / "{dataset}" / "{genomeAssembly}--{annotation}_export.Rds")`'}], 'params': [{'setup': '`sm cfg.AS.getWorkdir() + "/config.R"`'}], 'input': [{'annotation': '`sm cfg.getProcessedDataDir() + "/preprocess/{annotation}/txdb.db"`'}, {'fds_theta': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/savedObjects/raw-local-{dataset}/theta.h5"`'}], 'output': [{'k_counts': '`sm expand(cfg.exportCounts.getFilePattern(str_=True, expandStr=True) + "/k_{metric}_counts.tsv.gz", metric=["j", "theta"])`'}, {'n_counts': '`sm expand(cfg.exportCounts.getFilePattern(str_=True, expandStr=True) + "/n_{metric}_counts.tsv.gz", metric=["psi5", "psi3", "theta"])`'}], 'type': 'script'}}}, {'file': 'Scripts/AberrantSplicing/pipeline/FRASER/04_fit_hyperparameters_FraseR.R', 'outputFile': '/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/htmlOutput/Scripts_AberrantSplicing_pipeline_FRASER_04_fit_hyperparameters_FraseR.html', 'param': {'title': 'Hyper parameter optimization', 'author': 'Christian Mertes', 'wb': {'log': [{'snakemake': '`sm str(tmp_dir / "AS" / "{dataset}" / "04_hyper.Rds")`'}], 'params': [{'setup': '`sm cfg.AS.getWorkdir() + "/config.R"`'}, {'workingDir': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/"`'}], 'threads': 12, 'input': [{'filter': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/savedObjects/{dataset}/filter.done" `'}], 'output': [{'hyper': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/savedObjects/{dataset}/hyper.done" `'}], 'type': 'script'}}}, {'file': 'Scripts/AberrantSplicing/pipeline/FRASER/05_fit_autoencoder_FraseR.R', 'outputFile': '/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/htmlOutput/Scripts_AberrantSplicing_pipeline_FRASER_05_fit_autoencoder_FraseR.html', 'param': {'title': 'Fitting the autoencoder', 'author': 'Christian Mertes', 'wb': {'log': [{'snakemake': '`sm str(tmp_dir / "AS" / "{dataset}" / "05_fit.Rds")`'}], 'params': [{'setup': '`sm cfg.AS.getWorkdir() + "/config.R"`'}, {'workingDir': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/"`'}], 'threads': 20, 'input': [{'hyper': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/savedObjects/{dataset}/hyper.done" `'}], 'output': [{'fdsout': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/savedObjects/{dataset}/predictedMeans_theta.h5"`'}], 'type': 'script'}}}, {'file': 'Scripts/AberrantSplicing/pipeline/FRASER/06_calculation_stats_AE_FraseR.R', 'outputFile': '/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/htmlOutput/Scripts_AberrantSplicing_pipeline_FRASER_06_calculation_stats_AE_FraseR.html', 'param': {'title': 'Calculate P values', 'author': 'Christian Mertes', 'wb': {'log': [{'snakemake': '`sm str(tmp_dir / "AS" / "{dataset}" / "06_stats.Rds")`'}], 'params': [{'setup': '`sm cfg.AS.getWorkdir() + "/config.R"`'}, {'workingDir': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/"`'}], 'threads': 20, 'input': [{'fdsin': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/savedObjects/{dataset}/" + "predictedMeans_theta.h5"`'}], 'output': [{'fdsout': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/savedObjects/{dataset}/" + "padjBetaBinomial_theta.h5"`'}], 'type': 'script'}}}, {'file': 'Scripts/AberrantSplicing/pipeline/FRASER/07_extract_results_FraseR.R', 'outputFile': '/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/htmlOutput/Scripts_AberrantSplicing_pipeline_FRASER_07_extract_results_FraseR.html', 'param': {'title': 'Results of FRASER analysis', 'author': 'Christian Mertes', 'wb': {'log': [{'snakemake': '`sm str(tmp_dir / "AS" / "{dataset}--{annotation}" / "07_results.Rds")`'}], 'params': [{'workingDir': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/"`'}, {'outputDir': '`sm cfg.getProcessedResultsDir() + "/aberrant_splicing/datasets/"`'}, {'padjCutoff': '`sm cfg.AS.get("padjCutoff")`'}, {'zScoreCutoff': '`sm cfg.AS.get("zScoreCutoff")`'}, {'deltaPsiCutoff': '`sm cfg.AS.get("deltaPsiCutoff")`'}, {'hpoFile': '`sm cfg.get("hpoFile")`'}], 'threads': 10, 'input': [{'setup': '`sm cfg.AS.getWorkdir() + "/config.R"`'}, {'add_HPO_cols': '`sm str(projectDir / ".drop" / "helpers" / "add_HPO_cols.R")`'}, {'fdsin': '`sm cfg.getProcessedDataDir() + "/aberrant_splicing/datasets/savedObjects/{dataset}/" + "padjBetaBinomial_theta.h5"`'}, {'txdb': '`sm cfg.getProcessedDataDir() + "/preprocess/{annotation}/txdb.db"`'}, {'gene_name_mapping': '`sm cfg.getProcessedDataDir() + "/preprocess/{annotation}/gene_name_mapping_{annotation}.tsv"`'}], 'output': [{'resultTableJunc': '`sm cfg.getProcessedResultsDir() + "/aberrant_splicing/results/{annotation}/fraser/{dataset}/results_per_junction.tsv"`'}, {'resultTableGene': '`sm cfg.getProcessedResultsDir() + "/aberrant_splicing/results/{annotation}/fraser/{dataset}/results.tsv"`'}, {'fds': '`sm cfg.getProcessedResultsDir() + "/aberrant_splicing/datasets/savedObjects/{dataset}--{annotation}/fds-object.RDS"`'}], 'type': 'script'}}}, {'file': 'Scripts/AberrantSplicing/pipeline/FRASER/Datasets.R', 'outputFile': '/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/htmlOutput/Scripts_AberrantSplicing_pipeline_FRASER_Datasets.html', 'param': {'title': 'Full FRASER analysis over all datasets', 'wb': {'log': [{'snakemake': '`sm str(tmp_dir / "AS" / "FRASER_datasets.Rds")`'}], 'input': [{'fraser_summary': '`sm expand(config["htmlOutputPath"] + "/AberrantSplicing/{dataset}--{annotation}_summary.html", annotation=cfg.genome.getGeneVersions(), dataset=cfg.AS.groups)`'}]}, 'output': 'html_document'}}, {'file': 'Scripts/AberrantSplicing/pipeline/FRASER/Summary.R', 'outputFile': '/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/htmlOutput/Scripts_AberrantSplicing_pipeline_FRASER_Summary.html', 'param': {'title': "FRASER Summary: `r paste(snakemake@wildcards$dataset, snakemake@wildcards$annotation, sep = '--')`", 'author': 'mumichae, vyepez, ischeller', 'wb': {'log': [{'snakemake': '`sm str(tmp_dir / "AS" / "{dataset}--{annotation}" / "FRASER_summary.Rds")`'}], 'params': [{'setup': '`sm cfg.AS.getWorkdir() + "/config.R"`'}], 'input': [{'fdsin': '`sm cfg.getProcessedResultsDir() + "/aberrant_splicing/datasets/savedObjects/{dataset}--{annotation}/fds-object.RDS"`'}, {'results': '`sm cfg.getProcessedResultsDir() + "/aberrant_splicing/results/{annotation}/fraser/{dataset}/results.tsv"`'}], 'output': [{'wBhtml': '`sm config["htmlOutputPath"] + "/AberrantSplicing/{dataset}--{annotation}_summary.html"`'}, {'res_html': '`sm config["htmlOutputPath"] + "/AberrantSplicing/FRASER_results_{dataset}--{annotation}.tsv"`'}], 'type': 'noindex'}}}, {'file': 'Scripts/Pipeline/SampleAnnotation.R', 'outputFile': '/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/htmlOutput/Scripts_Pipeline_SampleAnnotation.html', 'param': {'title': 'Sample Annotation Overview', 'author': None, 'wb': {'log': [{'snakemake': '`sm str(tmp_dir / "SampleAnnotation.Rds")`'}], 'params': [{'hpoFile': '`sm cfg.get("hpoFile")`'}], 'input': [{'sampleAnnotation': '`sm sa.file`'}], 'output': [{'hpoOverlap': '`sm touch(cfg.getProcessedDataDir() + "/sample_anno/genes_overlapping_HPO_terms.tsv")`'}]}, 'output': {'html_document': {'code_folding': 'hide', 'code_download': True}}}}, {'file': 'Scripts/Pipeline/preprocessGeneAnnotation.R', 'outputFile': '/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/htmlOutput/Scripts_Pipeline_preprocessGeneAnnotation.html', 'param': {'title': 'Preprocess Gene Annotations', 'author': 'mumichae', 'wb': {'log': [{'snakemake': '`sm str(tmp_dir / "AE" / "{annotation}" / "preprocess.Rds")`'}], 'input': [{'gtf': '`sm lambda wildcards: cfg.genome.getGeneAnnotationFile(wildcards.annotation) `'}], 'output': [{'txdb': '`sm cfg.getProcessedDataDir() + "/preprocess/{annotation}/txdb.db"`'}, {'gene_name_mapping': '`sm cfg.getProcessedDataDir() + "/preprocess/{annotation}/gene_name_mapping_{annotation}.tsv"`'}, {'count_ranges': '`sm cfg.getProcessedDataDir() + "/aberrant_expression/{annotation}/count_ranges.Rds" `'}], 'type': 'script'}}}]
Finding .md files:

Found files in scope of wBuild: ['Scripts/AberrantSplicing/pipeline/aberrant_splicing_readme.md'].

Found /pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/htmlOutput/Scripts_AberrantSplicing_pipeline_aberrant_splicing_readme.html.

Found /pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/htmlOutput/readme.html.

Dependencies file generated at: /tmp/tmpouiqzdh4

Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 1 (use --cores to define parallelism)
Rules claiming more threads will be scaled down.
Job stats:
job                                                                            count    min threads    max threads
---------------------------------------------------------------------------  -------  -------------  -------------
AberrantSplicing_Overview_R                                                        1              1              1
AberrantSplicing_pipeline_Counting_00_define_datasets_from_anno_R                  1              1              1
AberrantSplicing_pipeline_Counting_01_0_countRNA_init_R                            1              1              1
AberrantSplicing_pipeline_Counting_01_1_countRNA_splitReads_samplewise_R          20              1              1
AberrantSplicing_pipeline_Counting_01_2_countRNA_splitReads_merge_R                1              1              1
AberrantSplicing_pipeline_Counting_01_3_countRNA_nonSplitReads_samplewise_R       20              1              1
AberrantSplicing_pipeline_Counting_01_4_countRNA_nonSplitReads_merge_R             1              1              1
AberrantSplicing_pipeline_Counting_01_5_countRNA_collect_R                         1              1              1
AberrantSplicing_pipeline_Counting_02_psi_value_calculation_FraseR_R               1              1              1
AberrantSplicing_pipeline_Counting_03_filter_expression_FraseR_R                   1              1              1
AberrantSplicing_pipeline_Counting_DatasetsF_R                                     1              1              1
AberrantSplicing_pipeline_Counting_Summary_R                                       1              1              1
AberrantSplicing_pipeline_FRASER_04_fit_hyperparameters_FraseR_R                   1              1              1
AberrantSplicing_pipeline_FRASER_05_fit_autoencoder_FraseR_R                       1              1              1
AberrantSplicing_pipeline_FRASER_06_calculation_stats_AE_FraseR_R                  1              1              1
AberrantSplicing_pipeline_FRASER_07_extract_results_FraseR_R                       1              1              1
AberrantSplicing_pipeline_FRASER_Datasets_R                                        1              1              1
AberrantSplicing_pipeline_FRASER_Summary_R                                         1              1              1
Index                                                                              1              1              1
aberrantSplicing                                                                   1              1              1
aberrantSplicing_dependency                                                        1              1              1
all                                                                                1              1              1
dependencyGraph                                                                    1              1              1
total                                                                             61              1              1

Resources before job selection: {'_cores': 1, '_nodes': 9223372036854775807}
Ready jobs (2):
	AberrantSplicing_pipeline_Counting_00_define_datasets_from_anno_R
	aberrantSplicing_dependency
Select jobs to execute...
Selected jobs (1):
	AberrantSplicing_pipeline_Counting_00_define_datasets_from_anno_R
Resources after job selection: {'_cores': 0, '_nodes': 9223372036854775806}

[Mon Apr 17 14:17:16 2023]
rule AberrantSplicing_pipeline_Counting_00_define_datasets_from_anno_R:
    input: /pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/sample_annotation/fpf_test_sample_annotation.tsv, Scripts/AberrantSplicing/pipeline/Counting/00_define_datasets_from_anno.R
    output: /pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/processed_data/aberrant_splicing/annotations/group1.tsv, /pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/htmlOutput/AberrantSplicing/annotations/group1.html
    log: /nas/weka.gel.zone/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/.drop/tmp/AS/group1/00_defineDataset.Rds
    jobid: 12
    reason: Params have changed since last execution
    wildcards: dataset=group1
    resources: tmpdir=/tmp

Loading required package: knitr
Loading required package: rmarkdown


processing file: /tmp/RtmpqaMWTP/file20b65a5bc11c/00_define_datasets_from_anno.spin.Rmd
output file: /tmp/RtmpqaMWTP/file20b65a5bc11c/00_define_datasets_from_anno.knit.md


Output created: /tmp/RtmpqaMWTP/file20b64a078c16/group1.html
Warning message:
In png(..., res = dpi, units = "in") :
  unable to open connection to X11 display ''
[Mon Apr 17 14:17:59 2023]
Finished job 12.
1 of 61 steps (2%) done
Resources before job selection: {'_cores': 1, '_nodes': 9223372036854775807}
Ready jobs (2):
	AberrantSplicing_pipeline_Counting_01_0_countRNA_init_R
	aberrantSplicing_dependency
Select jobs to execute...
Selected jobs (1):
	AberrantSplicing_pipeline_Counting_01_0_countRNA_init_R
Resources after job selection: {'_cores': 0, '_nodes': 9223372036854775806}

[Mon Apr 17 14:17:59 2023]
rule AberrantSplicing_pipeline_Counting_01_0_countRNA_init_R:
    input: /pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/processed_data/aberrant_splicing/annotations/group1.tsv, Scripts/AberrantSplicing/pipeline/Counting/01_0_countRNA_init.R
    output: /pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/processed_data/aberrant_splicing/datasets/savedObjects/raw-local-group1/fds-object.RDS, /pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/processed_data/aberrant_splicing/datasets/cache/raw-local-group1/fds.done
    log: /nas/weka.gel.zone/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/.drop/tmp/AS/group1/01_0_init.Rds
    jobid: 11
    reason: Input files updated by another job: /pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/processed_data/aberrant_splicing/annotations/group1.tsv
    wildcards: dataset=group1
    resources: tmpdir=/tmp

Load packages
Mon Apr 17 14:18:33 2023: Writing final FRASER object ('/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/processed_data/aberrant_splicing/datasets//savedObjects/raw-local-group1/fds-object.RDS').
Mon Apr 17 14:18:33 2023: FRASER object initialized for group1
[Mon Apr 17 14:18:36 2023]
Finished job 11.
2 of 61 steps (3%) done
Resources before job selection: {'_cores': 1, '_nodes': 9223372036854775807}
Ready jobs (21):
	AberrantSplicing_pipeline_Counting_01_1_countRNA_splitReads_samplewise_R
	AberrantSplicing_pipeline_Counting_01_1_countRNA_splitReads_samplewise_R
	AberrantSplicing_pipeline_Counting_01_1_countRNA_splitReads_samplewise_R
	AberrantSplicing_pipeline_Counting_01_1_countRNA_splitReads_samplewise_R
	AberrantSplicing_pipeline_Counting_01_1_countRNA_splitReads_samplewise_R
	AberrantSplicing_pipeline_Counting_01_1_countRNA_splitReads_samplewise_R
	AberrantSplicing_pipeline_Counting_01_1_countRNA_splitReads_samplewise_R
	AberrantSplicing_pipeline_Counting_01_1_countRNA_splitReads_samplewise_R
	AberrantSplicing_pipeline_Counting_01_1_countRNA_splitReads_samplewise_R
	AberrantSplicing_pipeline_Counting_01_1_countRNA_splitReads_samplewise_R
	AberrantSplicing_pipeline_Counting_01_1_countRNA_splitReads_samplewise_R
	aberrantSplicing_dependency
	AberrantSplicing_pipeline_Counting_01_1_countRNA_splitReads_samplewise_R
	AberrantSplicing_pipeline_Counting_01_1_countRNA_splitReads_samplewise_R
	AberrantSplicing_pipeline_Counting_01_1_countRNA_splitReads_samplewise_R
	AberrantSplicing_pipeline_Counting_01_1_countRNA_splitReads_samplewise_R
	AberrantSplicing_pipeline_Counting_01_1_countRNA_splitReads_samplewise_R
	AberrantSplicing_pipeline_Counting_01_1_countRNA_splitReads_samplewise_R
	AberrantSplicing_pipeline_Counting_01_1_countRNA_splitReads_samplewise_R
	AberrantSplicing_pipeline_Counting_01_1_countRNA_splitReads_samplewise_R
	AberrantSplicing_pipeline_Counting_01_1_countRNA_splitReads_samplewise_R
Select jobs to execute...
Selected jobs (1):
	AberrantSplicing_pipeline_Counting_01_1_countRNA_splitReads_samplewise_R
Resources after job selection: {'_cores': 0, '_nodes': 9223372036854775806}

[Mon Apr 17 14:18:36 2023]
rule AberrantSplicing_pipeline_Counting_01_1_countRNA_splitReads_samplewise_R:
    input: /pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/processed_data/aberrant_splicing/datasets/cache/raw-local-group1/fds.done, Scripts/AberrantSplicing/pipeline/Counting/01_1_countRNA_splitReads_samplewise.R
    output: /pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/processed_data/aberrant_splicing/datasets/cache/raw-local-group1/sample_tmp/splitCounts/sample_LP5001322-RNA_E02.done
    log: /nas/weka.gel.zone/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/.drop/tmp/AS/group1/splitReads/LP5001322-RNA_E02.Rds
    jobid: 14
    reason: Missing output files: /pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/processed_data/aberrant_splicing/datasets/cache/raw-local-group1/sample_tmp/splitCounts/sample_LP5001322-RNA_E02.done; Input files updated by another job: /pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/processed_data/aberrant_splicing/datasets/cache/raw-local-group1/fds.done
    wildcards: dataset=group1, sample_id=LP5001322-RNA_E02
    resources: tmpdir=/tmp

Load packages
Loading required package: rtracklayer

Attaching package: ‘rtracklayer’

The following object is masked from ‘package:plotly’:

    export

Mon Apr 17 14:19:10 2023: Count split reads for sample: LP5001322-RNA_E02
Error in asMethod(object) :
  The character vector to convert to a GRanges object must contain
  strings of the form "chr:start-end" or "chr:start-end:strand", with end
  >= start - 1, or "chr:pos" or "chr:pos:strand". For example:
  "chr1:2501-2900", "chr1:2501-2900:+", or "chr1:740". Note that ".." is
  a valid alternate start/end separator. Strand can be "+", "-", "*", or
  missing.
Calls: countSplitReads -> GRanges -> as -> asMethod
Execution halted
Full Traceback (most recent call last):
  File "/resources/tools/apps/software/lang/Anaconda3/home/2021.11/envs/drop_env_1.2.4/lib/python3.8/site-packages/snakemake/executors/__init__.py", line 2578, in run_wrapper
    run(
  File "/tmp/tmpouiqzdh4", line 96, in __rule_AberrantSplicing_pipeline_Counting_01_1_countRNA_splitReads_samplewise_R
    script: '/resources/tools/apps/software/lang/Anaconda3/home/2021.11/envs/drop_env_1.2.4/lib/python3.8/site-packages/wbuild/R/wBRender.R'
  File "/resources/tools/apps/software/lang/Anaconda3/home/2021.11/envs/drop_env_1.2.4/lib/python3.8/site-packages/snakemake/script.py", line 1559, in script
    executor.evaluate()
  File "/resources/tools/apps/software/lang/Anaconda3/home/2021.11/envs/drop_env_1.2.4/lib/python3.8/site-packages/snakemake/script.py", line 462, in evaluate
    self.execute_script(fd.name, edit=edit)
  File "/resources/tools/apps/software/lang/Anaconda3/home/2021.11/envs/drop_env_1.2.4/lib/python3.8/site-packages/snakemake/script.py", line 811, in execute_script
    self._execute_cmd("Rscript --vanilla {fname:q}", fname=fname)
  File "/resources/tools/apps/software/lang/Anaconda3/home/2021.11/envs/drop_env_1.2.4/lib/python3.8/site-packages/snakemake/script.py", line 493, in _execute_cmd
    return shell(
  File "/resources/tools/apps/software/lang/Anaconda3/home/2021.11/envs/drop_env_1.2.4/lib/python3.8/site-packages/snakemake/shell.py", line 300, in __new__
    raise sp.CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command 'set -euo pipefail;  Rscript --vanilla /nas/weka.gel.zone/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/.snakemake/scripts/tmppb08iij8.01_1_countRNA_splitReads_samplewise.R' returned non-zero exit status 1.

[Mon Apr 17 14:19:12 2023]
Error in rule AberrantSplicing_pipeline_Counting_01_1_countRNA_splitReads_samplewise_R:
    jobid: 14
    input: /pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/processed_data/aberrant_splicing/datasets/cache/raw-local-group1/fds.done, Scripts/AberrantSplicing/pipeline/Counting/01_1_countRNA_splitReads_samplewise.R
    output: /pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/processed_data/aberrant_splicing/datasets/cache/raw-local-group1/sample_tmp/splitCounts/sample_LP5001322-RNA_E02.done
    log: /nas/weka.gel.zone/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/.drop/tmp/AS/group1/splitReads/LP5001322-RNA_E02.Rds (check log file(s) for error details)

Full Traceback (most recent call last):
  File "/resources/tools/apps/software/lang/Anaconda3/home/2021.11/envs/drop_env_1.2.4/lib/python3.8/site-packages/snakemake/executors/__init__.py", line 2578, in run_wrapper
    run(
  File "/tmp/tmpouiqzdh4", line 96, in __rule_AberrantSplicing_pipeline_Counting_01_1_countRNA_splitReads_samplewise_R
    script: '/resources/tools/apps/software/lang/Anaconda3/home/2021.11/envs/drop_env_1.2.4/lib/python3.8/site-packages/wbuild/R/wBRender.R'
  File "/resources/tools/apps/software/lang/Anaconda3/home/2021.11/envs/drop_env_1.2.4/lib/python3.8/site-packages/snakemake/script.py", line 1559, in script
    executor.evaluate()
  File "/resources/tools/apps/software/lang/Anaconda3/home/2021.11/envs/drop_env_1.2.4/lib/python3.8/site-packages/snakemake/script.py", line 462, in evaluate
    self.execute_script(fd.name, edit=edit)
  File "/resources/tools/apps/software/lang/Anaconda3/home/2021.11/envs/drop_env_1.2.4/lib/python3.8/site-packages/snakemake/script.py", line 811, in execute_script
    self._execute_cmd("Rscript --vanilla {fname:q}", fname=fname)
  File "/resources/tools/apps/software/lang/Anaconda3/home/2021.11/envs/drop_env_1.2.4/lib/python3.8/site-packages/snakemake/script.py", line 493, in _execute_cmd
    return shell(
  File "/resources/tools/apps/software/lang/Anaconda3/home/2021.11/envs/drop_env_1.2.4/lib/python3.8/site-packages/snakemake/shell.py", line 300, in __new__
    raise sp.CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command 'set -euo pipefail;  Rscript --vanilla /nas/weka.gel.zone/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/.snakemake/scripts/tmppb08iij8.01_1_countRNA_splitReads_samplewise.R' returned non-zero exit status 1.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/resources/tools/apps/software/lang/Anaconda3/home/2021.11/envs/drop_env_1.2.4/lib/python3.8/site-packages/snakemake/executors/__init__.py", line 667, in _callback
    raise ex
  File "/resources/tools/apps/software/lang/Anaconda3/home/2021.11/envs/drop_env_1.2.4/lib/python3.8/concurrent/futures/thread.py", line 57, in run
    result = self.fn(*self.args, **self.kwargs)
  File "/resources/tools/apps/software/lang/Anaconda3/home/2021.11/envs/drop_env_1.2.4/lib/python3.8/site-packages/snakemake/executors/__init__.py", line 653, in cached_or_run
    run_func(*args)
  File "/resources/tools/apps/software/lang/Anaconda3/home/2021.11/envs/drop_env_1.2.4/lib/python3.8/site-packages/snakemake/executors/__init__.py", line 2614, in run_wrapper
    raise RuleException(
snakemake.exceptions.RuleException: CalledProcessError in file /tmp/tmpouiqzdh4, line 36:
Command 'set -euo pipefail;  Rscript --vanilla /nas/weka.gel.zone/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/.snakemake/scripts/tmppb08iij8.01_1_countRNA_splitReads_samplewise.R' returned non-zero exit status 1.
  File "/tmp/tmpouiqzdh4", line 36, in __rule_AberrantSplicing_pipeline_Counting_01_1_countRNA_splitReads_samplewise_R

RuleException:
CalledProcessError in file /tmp/tmpouiqzdh4, line 36:
Command 'set -euo pipefail;  Rscript --vanilla /nas/weka.gel.zone/pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf_fraser/.snakemake/scripts/tmppb08iij8.01_1_countRNA_splitReads_samplewise.R' returned non-zero exit status 1.
  File "/tmp/tmpouiqzdh4", line 36, in __rule_AberrantSplicing_pipeline_Counting_01_1_countRNA_splitReads_samplewise_R
  File "/resources/tools/apps/software/lang/Anaconda3/home/2021.11/envs/drop_env_1.2.4/lib/python3.8/concurrent/futures/thread.py", line 57, in run
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: .snakemake/log/2023-04-17T141642.905954.snakemake.log
unlocking
removing lock
removing lock
removed all locks