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Commit 81a24580 authored by Gervaise Henry's avatar Gervaise Henry :cowboy:
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Harmonize in script comments

parent a37b535c
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2 merge requests!37v0.0.1,!33Resolve "process_qc"
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workflow/rna-seq.nf
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......@@ -176,39 +176,39 @@ process parseMetadata {
hostname > ${repRID}.parseMetadata.err
ulimit -a >> ${repRID}.parseMetadata.err
# Check replicate RID metadata
# check replicate RID metadata
rep=\$(python3 ${script_parseMeta} -r ${repRID} -m "${fileMeta}" -p repRID)
echo "LOG: replicate RID metadata parsed: \${rep}" >> ${repRID}.parseMetadata.err
# Get experiment RID metadata
# get experiment RID metadata
exp=\$(python3 ${script_parseMeta} -r ${repRID} -m "${fileMeta}" -p expRID)
echo "LOG: experiment RID metadata parsed: \${exp}" >> ${repRID}.parseMetadata.err
# Get study RID metadata
# get study RID metadata
study=\$(python3 ${script_parseMeta} -r ${repRID} -m "${fileMeta}" -p studyRID)
echo "LOG: study RID metadata parsed: \${study}" >> ${repRID}.parseMetadata.err
# Get endedness metadata
# get endedness metadata
endsMeta=\$(python3 ${script_parseMeta} -r ${repRID} -m "${experimentSettingsMeta}" -p endsMeta)
echo "LOG: endedness metadata parsed: \${endsMeta}" >> ${repRID}.parseMetadata.err
# Manually get endness
# ganually get endness
endsManual=\$(python3 ${script_parseMeta} -r ${repRID} -m "${fileMeta}" -p endsManual)
echo "LOG: endedness manually detected: \${endsManual}" >> ${repRID}.parseMetadata.err
# Get strandedness metadata
# get strandedness metadata
stranded=\$(python3 ${script_parseMeta} -r ${repRID} -m "${experimentSettingsMeta}" -p stranded)
echo "LOG: strandedness metadata parsed: \${stranded}" >> ${repRID}.parseMetadata.err
# Get spike-in metadata
# get spike-in metadata
spike=\$(python3 ${script_parseMeta} -r ${repRID} -m "${experimentSettingsMeta}" -p spike)
echo "LOG: spike-in metadata parsed: \${spike}" >> ${repRID}.parseMetadata.err
# Get species metadata
# get species metadata
species=\$(python3 ${script_parseMeta} -r ${repRID} -m "${experimentMeta}" -p species)
echo "LOG: species metadata parsed: \${species}" >> ${repRID}.parseMetadata.err
# Save design file
# gave design file
echo "\${endsMeta},\${endsManual},\${stranded},\${spike},\${species},\${exp},\${study}" > design.csv
"""
}
......@@ -260,7 +260,7 @@ process trimData {
hostname > ${repRID}.trimData.err
ulimit -a >> ${repRID}.trimData.err
#Trim fastq's using trim_galore
# trim fastq's using trim_galore
if [ "${ends}" == "se" ]
then
echo "LOG: running trim_galore using single-end settings" >> ${repRID}.trimData.err
......@@ -300,7 +300,7 @@ process getRefInfer {
ulimit -a >> ${repRID}.getRefInfer.err
export https_proxy=\${http_proxy}
#Set the reference name
# set the reference name
if [ "${refName}" == "ERCC" ]
then
references=\$(echo ${referenceBase}/ERCC${refERCCVersion})
......@@ -315,7 +315,8 @@ process getRefInfer {
exit 1
fi
mkdir ${refName}
#Retreive appropriate reference appropriate location
# retreive appropriate reference appropriate location
if [ ${referenceBase} == "s3://bicf-references" ]
then
echo "LOG: grabbing reference files from S3" >> ${repRID}.getRefInfer.err
......@@ -332,7 +333,7 @@ process getRefInfer {
ln -s "\${references}"/genome.gtf 1>> ${repRID}.getRefInfer.out 2>> ${repRID}.getRefInfer.err
fi
#Make blank bed folder for ERCC
# make blank bed folder for ERCC
if [ "${refName}" == "ERCC" ]
then
rm ${refName}/bed
......@@ -402,7 +403,7 @@ process alignSampleData {
hostname > ${repRID}.${ref}.alignSampleData.err
ulimit -a >> ${repRID}.${ref}.alignSampleData.err
#Align the reads with Hisat 2
# align the reads with Hisat 2
if [ "${ends}" == "se" ]
then
echo "LOG: running Hisat2 with single-end settings" >> ${repRID}.${ref}.alignSampleData.err
......@@ -413,15 +414,15 @@ process alignSampleData {
hisat2 -p `nproc` --add-chrname -S ${ref}.sampled.sam -x hisat2/genome --no-mixed --no-discordant -1 ${fastq1} -2 ${fastq2} --summary-file ${ref}.alignSampleSummary.txt --new-summary 1>> ${repRID}.${ref}.alignSampleData.out 2>> ${repRID}.${ref}.alignSampleData.err
fi
#Convert the output sam file to a sorted bam file using Samtools
# convert the output sam file to a sorted bam file using Samtools
echo "LOG: converting from sam to bam" >> ${repRID}.${ref}.alignSampleData.err
samtools view -1 -@ `nproc` -F 4 -F 8 -F 256 -o ${ref}.sampled.bam ${ref}.sampled.sam 1>> ${repRID}.${ref}.alignSampleData.out 2>> ${repRID}.${ref}.alignSampleData.err;
#Sort the bam file using Samtools
# sort the bam file using Samtools
echo "LOG: sorting the bam file" >> ${repRID}.${ref}.alignSampleData.err
samtools sort -@ `nproc` -O BAM -o ${ref}.sampled.sorted.bam ${ref}.sampled.bam 1>> ${repRID}.${ref}.alignSampleData.out 2>> ${repRID}.${ref}.alignSampleData.err;
#Index the sorted bam using Samtools
# index the sorted bam using Samtools
echo "LOG: indexing sorted bam file" >> ${repRID}.${ref}.alignSampleData.err
samtools index -@ `nproc` -b ${ref}.sampled.sorted.bam ${ref}.sampled.sorted.bam.bai 1>> ${repRID}.${ref}.alignSampleData.out 2>> ${repRID}.${ref}.alignSampleData.err;
"""
......@@ -588,7 +589,7 @@ process getRef {
ulimit -a >> ${repRID}.getRef.err
export https_proxy=\${http_proxy}
#Set the reference name
# set the reference name
if [ "${species}" == "Mus musculus" ]
then
references=\$(echo ${referenceBase}/GRCm${refMoVersion})
......@@ -608,7 +609,7 @@ process getRef {
fi
echo "LOG: species set to \${references}" >> ${repRID}.getRef.err
#Retreive appropriate reference appropriate location
# retreive appropriate reference appropriate location
if [ ${referenceBase} == "s3://bicf-references" ]
then
echo "LOG: grabbing reference files from S3" >> ${repRID}.getRef.err
......@@ -657,7 +658,7 @@ process alignData {
hostname > ${repRID}.align.err
ulimit -a >> ${repRID}.align.err
#Set stranded param for hisat2
# set stranded param for hisat2
if [ "${stranded}"=="unstranded" ]
then
strandedParam=""
......@@ -675,7 +676,7 @@ process alignData {
strandedParam="--rna-strandness RF"
fi
#Align the reads with Hisat 2
# align the reads with Hisat 2
if [ "${ends}" == "se" ]
then
echo "LOG: running Hisat2 with single-end settings" >> ${repRID}.align.err
......@@ -686,15 +687,15 @@ process alignData {
hisat2 -p `nproc` --add-chrname --un-gz ${repRID}.unal.gz -S ${repRID}.sam -x hisat2/genome \${strandedParam} --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
# convert the output sam file to a sorted bam file using Samtools
echo "LOG: converting from sam to bam" >> ${repRID}.align.err
samtools view -1 -@ `nproc` -F 4 -F 8 -F 256 -o ${repRID}.bam ${repRID}.sam 1>> ${repRID}.align.out 2>> ${repRID}.align.err;
#Sort the bam file using Samtools
# sort the bam file using Samtools
echo "LOG: sorting the bam file" >> ${repRID}.align.err
samtools sort -@ `nproc` -O BAM -o ${repRID}.sorted.bam ${repRID}.bam 1>> ${repRID}.align.out 2>> ${repRID}.align.err;
#Index the sorted bam using Samtools
# index the sorted bam using Samtools
echo "LOG: indexing sorted bam file" >> ${repRID}.align.err
samtools index -@ `nproc` -b ${repRID}.sorted.bam ${repRID}.sorted.bam.bai 1>> ${repRID}.align.out 2>> ${repRID}.align.err;
"""
......@@ -731,13 +732,13 @@ process dedupData {
echo "LOG: running picard MarkDuplicates to remove duplicate reads" >> ${repRID}.dedup.err
java -jar /picard/build/libs/picard.jar MarkDuplicates I=${bam} O=${repRID}.deduped.bam M=${repRID}.deduped.Metrics.txt REMOVE_DUPLICATES=true 1>> ${repRID}.dedup.out 2>> ${repRID}.dedup.err
# Sort the bam file using Samtools
# sort the bam file using Samtools
samtools sort -@ `nproc` -O BAM -o ${repRID}.sorted.deduped.bam ${repRID}.deduped.bam 1>>${repRID}.dedup.out 2>> ${repRID}.dedup.err
# Index the sorted bam using Samtools
# index the sorted bam using Samtools
samtools index -@ `nproc` -b ${repRID}.sorted.deduped.bam ${repRID}.sorted.deduped.bam.bai 1>>${repRID}.dedup.out 2>> ${repRID}.dedup.err
# Split the deduped BAM file for multi-threaded tin calculation
# split the deduped BAM file for multi-threaded tin calculation
for i in `samtools view ${repRID}.sorted.deduped.bam | cut -f3 | sort | uniq`;
do
echo "echo \"LOG: splitting each chromosome into its own BAM and BAI files with Samtools\" >> ${repRID}.dedup.err; samtools view -b ${repRID}.sorted.deduped.bam \${i} > ${repRID}.sorted.deduped.\${i}.bam; samtools index -@ `nproc` -b ${repRID}.sorted.deduped.\${i}.bam ${repRID}.sorted.deduped.\${i}.bam.bai"
......@@ -772,7 +773,7 @@ process makeBigWig {
hostname > ${repRID}.makeBigWig.err
ulimit -a >> ${repRID}.makeBigWig.err
#Run bamCoverage
# run bamCoverage
echo "LOG: Running bigWig bamCoverage" >> ${repRID}.makeBigWig.err
bamCoverage -p `nproc` -b ${bam} -o ${repRID}.bw 1>> ${repRID}.makeBigWig.out 2>> ${repRID}.makeBigWig.err
"""
......@@ -803,7 +804,7 @@ process countData {
hostname > ${repRID}.countData.err
ulimit -a >> ${repRID}.countData.err
#Determine strandedness and setup strandig for countData
# determine strandedness and setup strandig for countData
stranding=0;
if [ "${stranded}" == "unstranded" ]
then
......@@ -818,19 +819,18 @@ process countData {
stranding=2
echo "LOG: strandedness set to forward stranded [2]" >> ${repRID}.countData.err
fi
#Run countData
echo "LOG: running countData on the data" >> ${repRID}.countData.err
# run featureCounts
echo "LOG: running featureCounts on the data" >> ${repRID}.countData.err
if [ "${ends}" == "se" ]
then
featureCounts -T `nproc` -a ./genome.gtf -G ./genome.fna -g 'gene_name' -o ${repRID}.countData -s \${stranding} -R SAM --primary --ignoreDup ${repRID}.sorted.deduped.bam 1>> ${repRID}.countData.out 2>> ${repRID}.countData.err
#featureCounts -R SAM -p -G ./genome.fna -T `nproc` -s \${stranding} -a ./genome.gtf -o ${repRID}.countData -g 'gene_name' --primary --ignoreDup ${repRID}.sorted.deduped.bam 1>> ${repRID}.countData.out 2>> ${repRID}.countData.err
elif [ "${ends}" == "pe" ]
then
featureCounts -T `nproc` -a ./genome.gtf -G ./genome.fna -g 'gene_name' -o ${repRID}.countData -s \${stranding} -p -B -R SAM --primary --ignoreDup ${repRID}.sorted.deduped.bam 1>> ${repRID}.countData.out 2>> ${repRID}.countData.err
#featureCounts -R SAM -p -G ./genome.fna -T `nproc` -s \${stranding} -a ./genome.gtf -o ${repRID}.countData -g 'gene_name' --primary --ignoreDup -B ${repRID}.sorted.deduped.bam 1>> ${repRID}.countData.out 2>> ${repRID}.countData.err
fi
#Calculate TPM from the resulting countData table
# calculate TPM from the resulting countData table
echo "LOG: calculating TPM with R" >> ${repRID}.countData.err
Rscript calculateTPM.R --count "${repRID}.countData" 1>> ${repRID}.countData.out 2>> ${repRID}.countData.err
"""
......@@ -841,7 +841,6 @@ process countData {
*/
process fastqc {
tag "${repRID}"
publishDir "${outDir}/fastqc", mode: 'copy', pattern: "*_fastqc.zip"
publishDir "${logsDir}", mode: 'copy', pattern: "${repRID}.fastqc.{out,err}"
input:
......@@ -943,9 +942,11 @@ process aggrQC {
hostname > ${repRID}.aggrQC.err
ulimit -a >> ${repRID}.aggrQC.err
# make RID table
echo -e "Replicate RID\tExperiment RID\tStudy RID" > rid.tsv
echo -e "${repRID}\t${expRID}\t${studyRID}" >> rid.tsv
# make metadata table
echo -e "Source\tSpecies\tEnds\tStranded\tSpike-in" > metadata.tsv
echo -e "Infered\t${speciesI}\t${endsI}\t${strandedI}\t${spikeI}" >> metadata.tsv
echo -e "Submitter\t${speciesM}\t${endsM}\t${strandedM}\t${spikeM}" >> metadata.tsv
......@@ -957,7 +958,7 @@ process aggrQC {
rm -f ${innerDistance}
fi
#run MultiQC
# run MultiQC
multiqc -c ${multiqcConfig} .
"""
}
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