From 551681691735931e01a2459cedd9fe4a0aeb8cc5 Mon Sep 17 00:00:00 2001
From: Blaise Li <blaise.li__git@nsup.org>
Date: Thu, 11 Jan 2018 09:40:20 +0100
Subject: [PATCH] Minor tweaks.
---
PRO-seq/PRO-seq.snakefile | 23 ++++++-----------------
small_RNA-seq/small_RNA-seq.snakefile | 8 ++------
2 files changed, 8 insertions(+), 23 deletions(-)
diff --git a/PRO-seq/PRO-seq.snakefile b/PRO-seq/PRO-seq.snakefile
index 96be2f3..8155de6 100644
--- a/PRO-seq/PRO-seq.snakefile
+++ b/PRO-seq/PRO-seq.snakefile
@@ -433,19 +433,14 @@ rule fuse_bams:
rule compute_coverage:
input:
- bam = rules.fuse_bams.output.sorted_bam,
+ sorted_bam = rules.fuse_bams.output.sorted_bam,
output:
coverage = OPJ(output_dir, "{trimmer}", aligner, "mapped_C_elegans", "{lib}_{rep}_on_C_elegans_coverage.txt"),
params:
genomelen = genomelen,
- log:
- coverage_log = OPJ(log_dir, "{trimmer}", "compute_coverage", "{lib}_{rep}.log"),
- coverage_err = OPJ(log_dir, "{trimmer}", "compute_coverage", "{lib}_{rep}.err"),
shell:
"""
- # genomelen=$(samtools view -H {input} | grep "^@SQ" | awk -F ":" '{{sum+=$3}} END {{print sum}}')
- # genomelen=$(samtools view -H {input} | grep -P '^@SQ' | cut -f 3 -d ':' | awk '{{sum+=$1}} END {{print sum}}')
- bases=$(samtools depth {input} | awk '{{sum += $3}} END {{print sum}}') || error_exit "samtools depth failed"
+ bases=$(samtools depth {input.sorted_bam} | awk '{{sum += $3}} END {{print sum}}') || error_exit "samtools depth failed"
python3 -c "print(${{bases}} / {params.genomelen})" > {output.coverage}
"""
@@ -540,17 +535,11 @@ rule htseq_count_reads:
annot = biotype2annot,
message:
"Counting {wildcards.orientation} {wildcards.biotype} reads for {wildcards.lib}_{wildcards.rep} with htseq-count."
+ benchmark:
+ OPJ(log_dir, "{trimmer}", "htseq_count_reads", "{lib}_{rep}_{biotype}_{orientation}_benchmark.txt")
log:
- log = OPJ(log_dir, "{trimmer}", "htseq_count_reads", "{lib}_{rep}.log"),
- err = OPJ(log_dir, "{trimmer}", "htseq_count_reads", "{lib}_{rep}.err")
- #shell:
- # """
- # annot="/pasteur/entites/Mhe/Genomes/C_elegans/Caenorhabditis_elegans/Ensembl/WBcel235/Annotation/Genes/{wildcards.biotype}.gtf"
- # converter="/pasteur/entites/Mhe/Genomes/C_elegans/Caenorhabditis_elegans/Ensembl/WBcel235/Annotation/Genes/genes_id2name.pickle"
- # cmd="htseq-count -f bam -s {params.stranded} -a 0 -t transcript -i gene_id {input.sorted_bam} ${{annot}} | tee {output.counts} | id2name.py ${{converter}} > {output.counts_converted}"
- # echo ${{cmd}}
- # eval ${{cmd}} > {log}
- # """
+ log = OPJ(log_dir, "{trimmer}", "htseq_count_reads", "{lib}_{rep}_{biotype}_{orientation}.log"),
+ err = OPJ(log_dir, "{trimmer}", "htseq_count_reads", "{lib}_{rep}_{biotype}_{orientation}.err")
wrapper:
"file:///pasteur/homes/bli/src/bioinfo_utils/snakemake_wrappers/htseq_count_reads"
diff --git a/small_RNA-seq/small_RNA-seq.snakefile b/small_RNA-seq/small_RNA-seq.snakefile
index 4fb828b..2321af3 100644
--- a/small_RNA-seq/small_RNA-seq.snakefile
+++ b/small_RNA-seq/small_RNA-seq.snakefile
@@ -803,18 +803,14 @@ rule sam2indexedbam:
rule compute_coverage:
input:
- rules.sam2indexedbam.output.sorted_bam,
+ sorted_bam = rules.sam2indexedbam.output.sorted_bam,
output:
coverage = OPJ(output_dir, aligner, "mapped_C_elegans", "{lib}_{rep}", "{read_type}_on_C_elegans_coverage.txt"),
params:
genomelen = genomelen,
- # Currently not used
- #log:
- # log = OPJ(log_dir, "compute_coverage", "{lib}_{rep}_{read_type}.log"),
- # err = OPJ(log_dir, "compute_coverage", "{lib}_{rep}_{read_type}.err"),
shell:
"""
- bases=$(samtools depth {input} | awk '{{sum += $3}} END {{print sum}}') || error_exit "samtools depth failed"
+ bases=$(samtools depth {input.sorted_bam} | awk '{{sum += $3}} END {{print sum}}') || error_exit "samtools depth failed"
python3 -c "print(${{bases}} / {params.genomelen})" > {output.coverage}
"""
--
GitLab