chore(deps): pre-commit autoupdate

.pre-commit-config.yaml

@@ -36,7 +36,7 @@ repos:
         args: [--py39-plus]
 
   - repo: https://github.com/snakemake/snakefmt
-    rev: v2.0.1
+    rev: v2.0.3
     hooks:
       - id: snakefmt
 

workflow/Snakefile

@@ -63,8 +63,8 @@ include: "rules/common.smk"
 
 rule all:
     """
-General all rule to get all output files for MPRAsnakeflow (default rule).
-"""
+    General all rule to get all output files for MPRAsnakeflow (default rule).
+    """
     input:
         ## report
         getAssignmentConfig_helper(
@@ -183,8 +183,8 @@ General all rule to get all output files for MPRAsnakeflow (default rule).
 
 rule all_qc_report:
     """
-All rule to generate QC reports.
-"""
+    All rule to generate QC reports.
+    """
     input:
         getAssignmentConfig_helper(["results/assignment/{assignment}/qc_report.{config}.html"]),
         getOutputProjectConditionAssignmentConfig_helper(
@@ -194,8 +194,8 @@ All rule to generate QC reports.
 
 rule all_assignments:
     """
-All rule to get all output files for the assignments workflow.
-"""
+    All rule to get all output files for the assignments workflow.
+    """
     input:
         getAssignmentConfig_helper(
             [
@@ -213,8 +213,8 @@ All rule to get all output files for the assignments workflow.
 
 rule all_experiments:
     """
-All rule to get all output files for the experiment workflow.
-"""
+    All rule to get all output files for the experiment workflow.
+    """
     input:
         # stats BC nucleotide composition
         getOutputProjectConditionReplicateType_helper(
@@ -306,8 +306,8 @@ All rule to get all output files for the experiment workflow.
 
 rule all_experiments_counts_stats:
     """
-All rule to get count statistics of the experiment workflow.
-"""
+    All rule to get count statistics of the experiment workflow.
+    """
     input:
         getOutputProjectConditionReplicateType_helper(
             ["results/experiments/{project}/statistic/counts.freqUMIs.{condition}.{replicate}.{type}.txt"]
@@ -328,8 +328,8 @@ All rule to get count statistics of the experiment workflow.
 
 rule all_bc_overlap_statistic:
     """
-All rule to get BC overlap statistic of the experiment workflow.
-"""
+    All rule to get BC overlap statistic of the experiment workflow.
+    """
     input:
         getOutputProjectConfig_helper(
             ["results/experiments/{project}/statistic/bc_overlap.counts.{config}.tsv"],
@@ -345,8 +345,8 @@ All rule to get BC overlap statistic of the experiment workflow.
 
 rule all_experiments_assignments:
     """
-All rule to get assigned counts for experiment workflow.
-"""
+    All rule to get assigned counts for experiment workflow.
+    """
     input:
         getOutputProjectConditionAssignmentConfig_helper(
             [
@@ -359,8 +359,8 @@ All rule to get assigned counts for experiment workflow.
 
 rule all_experiments_assignments_statistic:
     """
-All rule to get assigned counts statistic for experiment workflow.
-"""
+    All rule to get assigned counts statistic for experiment workflow.
+    """
     input:
         getOutputProjectConditionAssignmentConfig_helper(
             [
@@ -382,8 +382,8 @@ All rule to get assigned counts statistic for experiment workflow.
 
 rule all_stats_BCNucleotideComposition:
     """
-All rule to get BC nucleotide composition of the experiment workflow.
-"""
+    All rule to get BC nucleotide composition of the experiment workflow.
+    """
     input:
         getOutputProjectConditionReplicateType_helper(
             ["results/experiments/{project}/statistic/counts/BCNucleotideComposition.{condition}.{replicate}.{type}.tsv.gz"]
@@ -392,8 +392,8 @@ All rule to get BC nucleotide composition of the experiment workflow.
 
 rule all_variants:
     """
-All rule to get variant effects of the experiment workflow.
-"""
+    All rule to get variant effects of the experiment workflow.
+    """
     input:
         getOutputVariants_helper(
             ["results/experiments/{project}/statistic/variants/{assignment}/{config}/correlation_variantTable.tsv"],

workflow/rules/assignment.smk

@@ -14,9 +14,9 @@ include: "assignment/statistic.smk"
 
 rule assignment_check_design:
     """
-Check if the design file is correct and no duplicated sequences are present (FWD and reverse).
-Also check if no duplicated headers and no illegal characters in header.
-"""
+    Check if the design file is correct and no duplicated sequences are present (FWD and reverse).
+    Also check if no duplicated headers and no illegal characters in header.
+    """
     input:
         design=lambda wc: config["assignments"][wc.assignment]["design_file"],
         script=getScript("assignment/check_design_file.py"),
@@ -57,11 +57,11 @@ Also check if no duplicated headers and no illegal characters in header.
 
 rule assignment_fastq_split:
     """
-Split the fastq files into n files for parallelisation.
-n is given by split_read in the configuration file.
+    Split the fastq files into n files for parallelisation.
+    n is given by split_read in the configuration file.
 
-Runs only if the design file is correct.
-"""
+    Runs only if the design file is correct.
+    """
     input:
         fastq=lambda wc: getAssignmentRead(
             wc.assignment,
@@ -105,8 +105,8 @@ Runs only if the design file is correct.
 
 rule assignment_attach_idx:
     """
-Extract the index sequence and add it to the header.
-"""
+    Extract the index sequence and add it to the header.
+    """
     input:
         read="results/assignment/{assignment}/fastq/splits/{read}.split{split}.fastq.gz",
         BC="results/assignment/{assignment}/fastq/splits/BC.split{split}.fastq.gz",
@@ -138,8 +138,8 @@ Extract the index sequence and add it to the header.
 
 rule assignment_merge_NGmerge:
     """
-Merge the FWD, REV and BC fastq files into one using NGmerge.
-"""
+    Merge the FWD, REV and BC fastq files into one using NGmerge.
+    """
     input:
         FWD="results/assignment/{assignment}/fastq/splits/FWD.split{split}.BCattached.fastq.gz",
         REV="results/assignment/{assignment}/fastq/splits/REV.split{split}.BCattached.fastq.gz",
@@ -170,8 +170,8 @@ Merge the FWD, REV and BC fastq files into one using NGmerge.
 
 rule assignment_merge_fastqjoin:
     """
-Merge the FWD, REV and BC fastq files into one using fastq-join.
-"""
+    Merge the FWD, REV and BC fastq files into one using fastq-join.
+    """
     input:
         FWD="results/assignment/{assignment}/fastq/splits/FWD.split{split}.BCattached.fastq.gz",
         REV="results/assignment/{assignment}/fastq/splits/REV.split{split}.BCattached.fastq.gz",
@@ -201,8 +201,8 @@ include: "assignment/mapping_pbmm2.smk"
 
 rule assignment_collectBCs:
     """
-Get the barcodes.
-"""
+    Get the barcodes.
+    """
     input:
         lambda wc: (
             "results/assignment/{assignment}/BCs/barcodes.pbmm2.tsv"
@@ -234,9 +234,9 @@ Get the barcodes.
 
 rule assignment_filter:
     """
-Filter the barcodes file based on the config given in the config-file.
-FIXME: Limitation is that oligos cannot have a name ambiguous or other.
-"""
+    Filter the barcodes file based on the config given in the config-file.
+    FIXME: Limitation is that oligos cannot have a name ambiguous or other.
+    """
     input:
         assignment="results/assignment/{assignment}/barcodes_incl_other.tsv.gz",
         script=getScript("assignment/filterAssignmentTsv.py"),

workflow/rules/assignment/hybridFWDRead.smk

@@ -6,8 +6,8 @@ This sankefile will extract the BC and FWD read from the hybrid read.
 
 rule assignment_hybridFWDRead_get_reads_by_length:
     """
-Get the barcode and read from the FWD read using fixed length
-"""
+    Get the barcode and read from the FWD read using fixed length
+    """
     input:
         fastq=lambda wc: (
             "results/assignment/{assignment}/fastq/FWD.trimmed.fastq.gz"
@@ -44,9 +44,9 @@ Get the barcode and read from the FWD read using fixed length
 
 rule assignment_hybridFWDRead_get_reads_by_cutadapt:
     """
-Get the barcode and read from the FWD read using cutadapt.
-Uses the paired end mode of cutadapt to write the FWD and BC read.
-"""
+    Get the barcode and read from the FWD read using cutadapt.
+    Uses the paired end mode of cutadapt to write the FWD and BC read.
+    """
     input:
         lambda wc: (
             "results/assignment/{assignment}/fastq/FWD.trimmed.fastq.gz"

workflow/rules/assignment/mapping_bbmap.smk

@@ -20,8 +20,8 @@
 
 rule assignment_mapping_bbmap:
     """
-Map the reads to the reference and sort unsing bwa mem
-"""
+    Map the reads to the reference and sort unsing bwa mem
+    """
     input:
         reads=lambda wc: getMappingRead(wc.assignment),
         check="results/assignment/{assignment}/design_check.done",
@@ -46,18 +46,18 @@ Map the reads to the reference and sort unsing bwa mem
 
 rule assignment_mapping_bbmap_getBCs:
     """
-Get the barcodes.
+    Get the barcodes.
 
-BAM/SAM fields:
-- bc_string = $2;
-- ref_name = $3;
-- alignement_start = $4;
-- mapping_quality = $5;
-- cigar = $6;
-- aligned_sequence = $10;
-- edit_distance = $12;
-- alignment_score = $13;
-"""
+    BAM/SAM fields:
+    - bc_string = $2;
+    - ref_name = $3;
+    - alignement_start = $4;
+    - mapping_quality = $5;
+    - cigar = $6;
+    - aligned_sequence = $10;
+    - edit_distance = $12;
+    - alignment_score = $13;
+    """
     input:
         "results/assignment/{assignment}/bbmap/merge_split{split}.mapped.bam",
     output:

workflow/rules/assignment/mapping_bwa.smk

@@ -1,7 +1,7 @@
 rule assignment_mapping_bwa_ref:
     """
-Create mapping reference for BWA from design file.
-"""
+    Create mapping reference for BWA from design file.
+    """
     input:
         ref="results/assignment/{assignment}/reference/reference.fa",
         check="results/assignment/{assignment}/design_check.done",
@@ -25,8 +25,8 @@ Create mapping reference for BWA from design file.
 
 rule assignment_mapping_bwa:
     """
-Map the reads to the reference and sort unsing bwa mem
-"""
+    Map the reads to the reference and sort unsing bwa mem
+    """
     input:
         reads=lambda wc: getMappingRead(wc.assignment),
         reference="results/assignment/{assignment}/reference/reference.fa",
@@ -59,8 +59,8 @@ Map the reads to the reference and sort unsing bwa mem
 
 rule assignment_mapping_bwa_getBCs:
     """
-Get the barcodes.
-"""
+    Get the barcodes.
+    """
     input:
         "results/assignment/{assignment}/bwa/merge_split{split}.mapped.bam",
     output:
@@ -114,8 +114,8 @@ Get the barcodes.
 
 rule assignment_mapping_bwa_getBCs_additional_filter:
     """
-Get the barcodes with a python script to rescue alignments with 0 mapping quality according to bwa.
-"""
+    Get the barcodes with a python script to rescue alignments with 0 mapping quality according to bwa.
+    """
     input:
         bam="results/assignment/{assignment}/bwa/merge_split{split}.mapped.bam",
         script=getScript("assignment/filter_bc_from_bam.py"),
@@ -146,8 +146,8 @@ Get the barcodes with a python script to rescue alignments with 0 mapping qualit
 
 rule assignment_collect:
     """
-Collect mapped reads.
-"""
+    Collect mapped reads.
+    """
     input:
         bams=lambda wc: expand(
             "results/assignment/{{assignment}}/{mapper}/merge_split{split}.mapped.bam",
@@ -169,8 +169,8 @@ Collect mapped reads.
 
 rule assignment_idx_bam:
     """
-Index the BAM file
-"""
+    Index the BAM file
+    """
     input:
         "results/assignment/{assignment}/aligned_merged_reads.bam",
     output:
@@ -187,8 +187,8 @@ Index the BAM file
 
 rule assignment_flagstat:
     """
-Run samtools flagstat
-"""
+    Run samtools flagstat
+    """
     input:
         bam="results/assignment/{assignment}/aligned_merged_reads.bam",
         idx="results/assignment/{assignment}/aligned_merged_reads.bam.bai",

workflow/rules/assignment/mapping_exact.smk

@@ -1,7 +1,7 @@
 rule assignment_mapping_exact_reference:
     """
-Create reference to map the exact design
-"""
+    Create reference to map the exact design
+    """
     input:
         check="results/assignment/{assignment}/design_check.done",
         ref="results/assignment/{assignment}/reference/reference.fa",
@@ -25,8 +25,8 @@ Create reference to map the exact design
 
 rule assignment_mapping_exact:
     """
-Map the reads to the reference and sort using exact match.
-"""
+    Map the reads to the reference and sort using exact match.
+    """
     input:
         reads=lambda wc: getMappingRead(wc.assignment),
         reference="results/assignment/{assignment}/reference/reference_exact.fa",