From 28f1a97fab76fac6a26f22c70f9875605934a81d Mon Sep 17 00:00:00 2001
From: s181706 <jonathan.gesell@utsouthwestern.edu>
Date: Fri, 20 Mar 2020 09:55:13 -0500
Subject: [PATCH] Code review changes/corrections
---
.gitlab-ci.yml | 2 +-
workflow/rna-seq.nf | 6 +++---
2 files changed, 4 insertions(+), 4 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 95ca346..3dbb78e 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -80,7 +80,7 @@ makeBigWig:
makeFeatureCounts:
stage: unit
script:
- - singularity run 'docker://bicf/subread2:2.0.0' featureCounts -R SAM -p -G /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/genome.fna -T `nproc` -a /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/genome.gtf -o Q-Y5JA_1M.se.featureCounts ./test_data/bam/small/Q-Y5JA_1M.se.sorted.deduped.bam
+ - singularity run 'docker://bicf/subread2:2.0.0' featureCounts -R SAM -p -G /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/genome.fna -T `nproc` -s 1 -a /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/genome.gtf -o Q-Y5JA_1M.se.featureCounts -g 'gene name' --primary --ignoreDup -B ./test_data/bam/small/Q-Y5JA_1M.se.sorted.deduped.bam
- singularity run 'docker://bicf/subread2:2.0.0' Rscript ./workflow/scripts/calculateTPM.R --count Q-Y5JA_1M.se.featureCounts
- pytest -m makeFeatureCounts
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index eaeff79..2285223 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -106,7 +106,7 @@ process getData {
echo "LOG: \${replicate}" >> ${repRID}.getData.err
# unzip bagit
- unzip ${bagit} 2>> ${repRID}.getData.err 1>> ${repRID}.getData.out 2>> ${repRID}.getData.err
+ unzip ${bagit} 1>> ${repRID}.getData.out 2>> ${repRID}.getData.err
echo "LOG: replicate bdbag unzipped" >> ${repRID}.getData.err
# bagit fetch fastq"s only and rename by repRID
@@ -337,7 +337,7 @@ process alignData {
elif [ "${endsManual_alignData}" == "pe" ]
then
echo "LOG: running Hisat2 with paired-end settings" >> ${repRID}.align.err
- hisat2 -p `nproc` --add-chrname --un-gz ${repRID}.unal.gz -S ${repRID}.sam -x hisat2/genome ${stranded_alignData} --no-mixed --no-discordant -1 ${fastq[0]} -2 ${fastq[1]} --summary-file ${repRID}.alignSummary.txt --new-summary 1>> ${repRID}.align.out 2> ${repRID}.align.err
+ hisat2 -p `nproc` --add-chrname --un-gz ${repRID}.unal.gz -S ${repRID}.sam -x hisat2/genome ${stranded_alignData} --no-mixed --no-discordant -1 ${fastq[0]} -2 ${fastq[1]} --summary-file ${repRID}.alignSummary.txt --new-summary 1>> ${repRID}.align.out 2>> ${repRID}.align.err
fi
#Convert the output sam file to a sorted bam file using Samtools
@@ -468,7 +468,7 @@ process makeFeatureCounts {
featureCounts -R SAM -p -G ./genome.fna -T `nproc` -s \${stranding} -a ./genome.gtf -o ${repRID}.featureCounts -g 'gene_name' --primary --ignoreDup ${repRID}.sorted.deduped.bam 1>> ${repRID}.makeFeatureCounts.out 2>> ${repRID}.makeFeatureCounts.err
elif [ "${endsManual_featureCounts }" == "pe" ]
then
- featureCounts -R SAM -p -G ./genmome.fna -T `nproc` -s \${stranding} -p -a ./genome.gtf -o ${repRID}.featureCounts -g 'gene_name' --primary --ignoreDup -B ${repRID}.sorted.deduped.bam 1>> ${repRID}.makeFeatureCounts.out 2>> ${repRID}.makeFeatureCounts.err
+ featureCounts -R SAM -p -G ./genmome.fna -T `nproc` -s \${stranding} -a ./genome.gtf -o ${repRID}.featureCounts -g 'gene_name' --primary --ignoreDup -B ${repRID}.sorted.deduped.bam 1>> ${repRID}.makeFeatureCounts.out 2>> ${repRID}.makeFeatureCounts.err
fi
#Calculate TMP from the resulting featureCounts table
--
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