RNA sequencing analysis pipeline using STAR, HISAT2 and Salmon with gene counts and quality control.

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nf-core-rnaseq
nf-core-rnaseq
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Introduction

nf-core/rnaseq is a bioinformatics pipeline that can be used to analyse RNA sequencing data obtained from organisms with a reference genome and annotation. It takes a samplesheet and FASTQ files as input, performs quality control (QC), trimming and (pseudo-)alignment, and produces a gene expression matrix and extensive QC report.

nf-core/rnaseq metro map

  1. Merge re-sequenced FastQ files ( cat )

  2. Sub-sample FastQ files and auto-infer strandedness ( fq , Salmon )

  3. Read QC ( FastQC )

  4. UMI extraction ( UMI-tools )

  5. Adapter and quality trimming ( Trim Galore! )

  6. Removal of genome contaminants ( BBSplit )

  7. Removal of ribosomal RNA ( SortMeRNA )

  8. Choice of multiple alignment and quantification routes:

    1. STAR -> Salmon

    2. STAR -> RSEM

    3. HiSAT2 -> NO QUANTIFICATION

  9. Sort and index alignments ( SAMtools )

  10. UMI-based deduplication ( UMI-tools )

  11. Duplicate read marking ( picard MarkDuplicates )

  12. Transcript assembly and quantification ( StringTie )

  13. Create bigWig coverage files ( BEDTools , bedGraphToBigWig )

  14. Extensive quality control:

    1. RSeQC

    2. Qualimap

    3. dupRadar

    4. Preseq

    5. DESeq2

  15. Pseudo-alignment and quantification ( Salmon ; optional )

  16. Present QC for raw read, alignment, gene biotype, sample similarity, and strand-specificity checks ( MultiQC , R )

Note The SRA download functionality has been removed from the pipeline ( >=3.2 ) and ported to an independent workflow called nf-core/fetchngs . You can provide --nf_core_pipeline rnaseq when running nf-core/fetchngs to download and auto-create a samplesheet containing publicly available samples that can be accepted directly as input by this pipeline.

Warning Quantification isn't performed if using --aligner hisat2 due to the lack of an appropriate option to calculate accurate expression estimates from HISAT2 derived genomic alignments. However, you can use this route if you have a preference for the alignment, QC and other types of downstream analysis compatible with the output of HISAT2.

Usage

Note If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup with -profile test before running the workflow on actual data.

First, prepare a samplesheet with your input data that looks as follows:

samplesheet.csv : 

sample,fastq_1,fastq_2,strandedness
CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,auto
CONTROL_REP1,AEG588A1_S1_L003_R1_001.fastq.gz,AEG588A1_S1_L003_R2_001.fastq.gz,auto
CONTROL_REP1,AEG588A1_S1_L004_R1_001.fastq.gz,AEG588A1_S1_L004_R2_001.fastq.gz,auto

Each row represents a fastq file (single-end) or a pair of fastq files (paired end). Rows with the same sample identifier are considered technical replicates and merged automatically. The strandedness refers to the library preparation and will be automatically inferred if set to auto .

Warning: Please provide pipeline parameters via the CLI or Nextflow -params-file option. Custom config files including those provided by the -c Nextflow option can be used to provide any configuration except for parameters ; see docs .

Now, you can run the pipeline using: 

nextflow run nf-core/rnaseq \
 --input samplesheet.csv \
 --outdir <OUTDIR> \
 --genome GRCh37 \
 -profile <docker/singularity/.../institute>

For more details, please refer to the usage documentation and the parameter documentation .

Pipeline output

To see the the results of a test run with a full size dataset refer to the results tab on the nf-core website pipeline page. For more details about the output files and reports, please refer to the output documentation .

Online videos

A short talk about the history, current status and functionality on offer in this pipeline was given by Harshil Patel ( @drpatelh ) on 8th February 2022 as part of the nf-core/bytesize series.

You can find numerous talks on the nf-core events page from various topics including writing pipelines/modules in Nextflow DSL2, using nf-core tooling, running nf-core pipelines as well as more generic content like contributing to Github. Please check them out!

Credits

These scripts were originally written for use at the National Genomics Infrastructure , part of SciLifeLab in Stockholm, Sweden, by Phil Ewels ( @ewels ) and Rickard Hammarén ( @Hammarn ).

The pipeline was re-written in Nextflow DSL2 and is primarily maintained by Harshil Patel ( @drpatelh ) from Seqera Labs, Spain .

The pipeline workflow diagram was designed by Sarah Guinchard ( @G-Sarah ) and James Fellows Yates ( @jfy133 ).

Many thanks to other who have helped out along the way too, including (but not limited to):

Contributions and Support

If you would like to contribute to this pipeline, please see the contributing guidelines .

For further information or help, don't hesitate to get in touch on the Slack #rnaseq channel (you can join with this invite ).

Citations

If you use nf-core/rnaseq for your analysis, please cite it using the following doi: 10.5281/zenodo.1400710

An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.

You can cite the nf-core publication as follows:

The nf-core framework for community-curated bioinformatics pipelines.

Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.

Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x .

Code Snippets

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"""
bedtools \\
    genomecov \\
    -ibam $bam \\
    -bg \\
    -strand + \\
    $args \\
    | bedtools sort > ${prefix_forward}.bedGraph

bedtools \\
    genomecov \\
    -ibam $bam \\
    -bg \\
    -strand - \\
    $args \\
    | bedtools sort > ${prefix_reverse}.bedGraph

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    bedtools: \$(bedtools --version | sed -e "s/bedtools v//g")
END_VERSIONS
"""
NextFlow BEDTools From line 31 of local/bedtools_genomecov.nf 
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"""
fasta2gtf.py \\
    -o ${add_fasta.baseName}.gtf \\
    $biotype_name \\
    $add_fasta

cat $fasta $add_fasta > ${name}.fasta
cat $gtf ${add_fasta.baseName}.gtf > ${name}.gtf

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    python: \$(python --version | sed 's/Python //g')
END_VERSIONS
"""
NextFlow From line 28 of local/cat_additional_fasta.nf 
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"""
deseq2_qc.r \\
    --count_file $counts \\
    --outdir ./ \\
    --cores $task.cpus \\
    $args

if [ -f "R_sessionInfo.log" ]; then
    sed "s/deseq2_pca/${label_lower}_deseq2_pca/g" <$pca_header_multiqc >tmp.txt
    sed -i -e "s/DESeq2 PCA/${label_upper} DESeq2 PCA/g" tmp.txt
    cat tmp.txt *.pca.vals.txt > ${label_lower}.pca.vals_mqc.tsv

    sed "s/deseq2_clustering/${label_lower}_deseq2_clustering/g" <$clustering_header_multiqc >tmp.txt
    sed -i -e "s/DESeq2 sample/${label_upper} DESeq2 sample/g" tmp.txt
    cat tmp.txt *.sample.dists.txt > ${label_lower}.sample.dists_mqc.tsv
fi

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    r-base: \$(echo \$(R --version 2>&1) | sed 's/^.*R version //; s/ .*\$//')
    bioconductor-deseq2: \$(Rscript -e "library(DESeq2); cat(as.character(packageVersion('DESeq2')))")
END_VERSIONS
"""
NextFlow DESeq2 From line 35 of local/deseq2_qc.nf 
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"""
dupradar.r \\
    $bam \\
    $prefix \\
    $gtf \\
    $strandedness \\
    $paired_end \\
    $task.cpus

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    r-base: \$(echo \$(R --version 2>&1) | sed 's/^.*R version //; s/ .*\$//')
    bioconductor-dupradar: \$(Rscript -e "library(dupRadar); cat(as.character(packageVersion('dupRadar')))")
END_VERSIONS
"""
NextFlow bioconductor-dupradar From line 33 of local/dupradar.nf 
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"""
gtf2bed \\
    $gtf \\
    > ${gtf.baseName}.bed

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    perl: \$(echo \$(perl --version 2>&1) | sed 's/.*v\\(.*\\)) built.*/\\1/')
END_VERSIONS
"""
NextFlow GFFutils From line 21 of local/gtf2bed.nf 
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"""
filter_gtf_for_genes_in_genome.py \\
    --gtf $gtf \\
    --fasta $fasta \\
    -o ${fasta.baseName}_genes.gtf

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    python: \$(python --version | sed 's/Python //g')
END_VERSIONS
"""
NextFlow From line 21 of local/gtf_gene_filter.nf 
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"""
cut -f 1,7 $count | tail -n +3 | cat $header - >> ${prefix}.biotype_counts_mqc.tsv

mqc_features_stat.py \\
    ${prefix}.biotype_counts_mqc.tsv \\
    -s $meta.id \\
    -f rRNA \\
    -o ${prefix}.biotype_counts_rrna_mqc.tsv

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    python: \$(python --version | sed 's/Python //g')
END_VERSIONS
"""
NextFlow From line 22 of local/multiqc_custom_biotype.nf 
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"""
multiqc \\
    -f \\
    $args \\
    $custom_config \\
    .

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" )
END_VERSIONS
"""
NextFlow MultiQC From line 60 of local/multiqc.nf 
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"""
$command $fasta | cut -d "|" -f1 > ${outfile}.fixed.fa

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    sed: \$(echo \$(sed --version 2>&1) | sed 's/^.*GNU sed) //; s/ .*\$//')
END_VERSIONS
"""
NextFlow From line 23 of local/preprocess_transcripts_fasta_gencode.nf 
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"""
mkdir -p tmp/genes
cut -f 1,2 `ls ./genes/* | head -n 1` > gene_ids.txt
for fileid in `ls ./genes/*`; do
    samplename=`basename \$fileid | sed s/\\.genes.results\$//g`
    echo \$samplename > tmp/genes/\${samplename}.counts.txt
    cut -f 5 \${fileid} | tail -n+2 >> tmp/genes/\${samplename}.counts.txt
    echo \$samplename > tmp/genes/\${samplename}.tpm.txt
    cut -f 6 \${fileid} | tail -n+2 >> tmp/genes/\${samplename}.tpm.txt
done

mkdir -p tmp/isoforms
cut -f 1,2 `ls ./isoforms/* | head -n 1` > transcript_ids.txt
for fileid in `ls ./isoforms/*`; do
    samplename=`basename \$fileid | sed s/\\.isoforms.results\$//g`
    echo \$samplename > tmp/isoforms/\${samplename}.counts.txt
    cut -f 5 \${fileid} | tail -n+2 >> tmp/isoforms/\${samplename}.counts.txt
    echo \$samplename > tmp/isoforms/\${samplename}.tpm.txt
    cut -f 6 \${fileid} | tail -n+2 >> tmp/isoforms/\${samplename}.tpm.txt
done

paste gene_ids.txt tmp/genes/*.counts.txt > rsem.merged.gene_counts.tsv
paste gene_ids.txt tmp/genes/*.tpm.txt > rsem.merged.gene_tpm.tsv
paste transcript_ids.txt tmp/isoforms/*.counts.txt > rsem.merged.transcript_counts.tsv
paste transcript_ids.txt tmp/isoforms/*.tpm.txt > rsem.merged.transcript_tpm.tsv

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    sed: \$(echo \$(sed --version 2>&1) | sed 's/^.*GNU sed) //; s/ .*\$//')
END_VERSIONS
"""
NextFlow From line 24 of local/rsem_merge_counts.nf 
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"""
salmon_summarizedexperiment.r \\
    NULL \\
    $counts \\
    $tpm

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    r-base: \$(echo \$(R --version 2>&1) | sed 's/^.*R version //; s/ .*\$//')
    bioconductor-summarizedexperiment: \$(Rscript -e "library(SummarizedExperiment); cat(as.character(packageVersion('SummarizedExperiment')))")
END_VERSIONS
"""
NextFlow From line 23 of local/salmon_summarizedexperiment.nf 
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"""
salmon_tx2gene.py \\
    --gtf $gtf \\
    --salmon salmon \\
    --id $params.gtf_group_features \\
    --extra $params.gtf_extra_attributes \\
    -o salmon_tx2gene.tsv

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    python: \$(python --version | sed 's/Python //g')
END_VERSIONS
"""
NextFlow Salmon From line 22 of local/salmon_tx2gene.nf 
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"""
salmon_tximport.r \\
    NULL \\
    salmon \\
    salmon.merged

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    r-base: \$(echo \$(R --version 2>&1) | sed 's/^.*R version //; s/ .*\$//')
    bioconductor-tximeta: \$(Rscript -e "library(tximeta); cat(as.character(packageVersion('tximeta')))")
END_VERSIONS
"""
NextFlow Salmon bioconductor-tximeta From line 26 of local/salmon_tximport.nf 
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"""
check_samplesheet.py \\
    $samplesheet \\
    samplesheet.valid.csv

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    python: \$(python --version | sed 's/Python //g')
END_VERSIONS
"""
NextFlow From line 21 of local/samplesheet_check.nf 
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"""
STAR \\
    --genomeDir $index \\
    --readFilesIn $reads  \\
    --runThreadN $task.cpus \\
    --outFileNamePrefix $prefix. \\
    $out_sam_type \\
    $ignore_gtf \\
    $seq_center \\
    $args

$mv_unsorted_bam

if [ -f ${prefix}.Unmapped.out.mate1 ]; then
    mv ${prefix}.Unmapped.out.mate1 ${prefix}.unmapped_1.fastq
    gzip ${prefix}.unmapped_1.fastq
fi
if [ -f ${prefix}.Unmapped.out.mate2 ]; then
    mv ${prefix}.Unmapped.out.mate2 ${prefix}.unmapped_2.fastq
    gzip ${prefix}.unmapped_2.fastq
fi

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    star: \$(STAR --version | sed -e "s/STAR_//g")
    samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
    gawk: \$(echo \$(gawk --version 2>&1) | sed 's/^.*GNU Awk //; s/, .*\$//')
END_VERSIONS
"""
NextFlow STAR From line 44 of local/star_align_igenomes.nf 
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"""
mkdir star
STAR \\
    --runMode genomeGenerate \\
    --genomeDir star/ \\
    --genomeFastaFiles $fasta \\
    --sjdbGTFfile $gtf \\
    --runThreadN $task.cpus \\
    $memory \\
    $args

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    star: \$(STAR --version | sed -e "s/STAR_//g")
    samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
    gawk: \$(echo \$(gawk --version 2>&1) | sed 's/^.*GNU Awk //; s/, .*\$//')
END_VERSIONS
"""
NextFlow STAR From line 26 of local/star_genomegenerate_igenomes.nf 
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"""
samtools faidx $fasta
NUM_BASES=`gawk '{sum = sum + \$2}END{if ((log(sum)/log(2))/2 - 1 > 14) {printf "%.0f", 14} else {printf "%.0f", (log(sum)/log(2))/2 - 1}}' ${fasta}.fai`

mkdir star
STAR \\
    --runMode genomeGenerate \\
    --genomeDir star/ \\
    --genomeFastaFiles $fasta \\
    --sjdbGTFfile $gtf \\
    --runThreadN $task.cpus \\
    --genomeSAindexNbases \$NUM_BASES \\
    $memory \\
    $args

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    star: \$(STAR --version | sed -e "s/STAR_//g")
    samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
    gawk: \$(echo \$(gawk --version 2>&1) | sed 's/^.*GNU Awk //; s/, .*\$//')
END_VERSIONS
"""
NextFlow SAMtools STAR From line 45 of local/star_genomegenerate_igenomes.nf 
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"""
prepare-for-rsem.py \\
    --stdin=$bam \\
    --stdout=${prefix}.bam \\
    --log=${prefix}.prepare_for_rsem.log \\
    $args

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    umitools: \$(umi_tools --version 2>&1 | sed 's/^.*UMI-tools version://; s/ *\$//')
END_VERSIONS
"""
NextFlow From line 24 of local/umitools_prepareforrsem.nf 
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"""
bbsplit.sh \\
    -Xmx${avail_mem}M \\
    ref_primary=$primary_ref \\
    ${other_refs.join(' ')} \\
    path=bbsplit \\
    threads=$task.cpus \\
    $args

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    bbmap: \$(bbversion.sh | grep -v "Duplicate cpuset")
END_VERSIONS
"""
NextFlow From line 44 of bbsplit/main.nf 
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"""
bbsplit.sh \\
    -Xmx${avail_mem}M \\
    $index_files \\
    threads=$task.cpus \\
    $fastq_in \\
    $fastq_out \\
    refstats=${prefix}.stats.txt \\
    $args

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    bbmap: \$(bbversion.sh | grep -v "Duplicate cpuset")
END_VERSIONS
"""
NextFlow From line 72 of bbsplit/main.nf 
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"""
cat ${readList.join(' ')} > ${prefix}.merged.fastq.gz

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    cat: \$(echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//')
END_VERSIONS
"""
NextFlow From line 26 of fastq/main.nf 
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"""
cat ${read1.join(' ')} > ${prefix}_1.merged.fastq.gz
cat ${read2.join(' ')} > ${prefix}_2.merged.fastq.gz

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    cat: \$(echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//')
END_VERSIONS
"""
NextFlow From line 40 of fastq/main.nf 
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"""
touch ${prefix}.merged.fastq.gz

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    cat: \$(echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//')
END_VERSIONS
"""
NextFlow From line 57 of fastq/main.nf 
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"""
touch ${prefix}_1.merged.fastq.gz
touch ${prefix}_2.merged.fastq.gz

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    cat: \$(echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//')
END_VERSIONS
"""
NextFlow From line 68 of fastq/main.nf 
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"""
samtools faidx $fasta
cut -f 1,2 ${fasta}.fai > ${fasta}.sizes

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    getchromsizes: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
NextFlow SAMtools From line 24 of getchromsizes/main.nf 
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"""
touch ${fasta}.fai
touch ${fasta}.sizes

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    getchromsizes: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
NextFlow From line 35 of getchromsizes/main.nf 
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"""
[ ! -f  ${prefix}.fastq.gz ] && ln -sf $reads ${prefix}.fastq.gz

fastp \\
    --stdout \\
    --in1 ${prefix}.fastq.gz \\
    --thread $task.cpus \\
    --json ${prefix}.fastp.json \\
    --html ${prefix}.fastp.html \\
    $adapter_list \\
    $fail_fastq \\
    $args \\
    2> ${prefix}.fastp.log \\
| gzip -c > ${prefix}.fastp.fastq.gz

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    fastp: \$(fastp --version 2>&1 | sed -e "s/fastp //g")
END_VERSIONS
"""
NextFlow fastp From line 36 of fastp/main.nf 
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"""
[ ! -f  ${prefix}.fastq.gz ] && ln -sf $reads ${prefix}.fastq.gz

fastp \\
    --in1 ${prefix}.fastq.gz \\
    --out1  ${prefix}.fastp.fastq.gz \\
    --thread $task.cpus \\
    --json ${prefix}.fastp.json \\
    --html ${prefix}.fastp.html \\
    $adapter_list \\
    $fail_fastq \\
    $args \\
    2> ${prefix}.fastp.log

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    fastp: \$(fastp --version 2>&1 | sed -e "s/fastp //g")
END_VERSIONS
"""
NextFlow fastp From line 57 of fastp/main.nf 
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"""
[ ! -f  ${prefix}_1.fastq.gz ] && ln -sf ${reads[0]} ${prefix}_1.fastq.gz
[ ! -f  ${prefix}_2.fastq.gz ] && ln -sf ${reads[1]} ${prefix}_2.fastq.gz
fastp \\
    --in1 ${prefix}_1.fastq.gz \\
    --in2 ${prefix}_2.fastq.gz \\
    --out1 ${prefix}_1.fastp.fastq.gz \\
    --out2 ${prefix}_2.fastp.fastq.gz \\
    --json ${prefix}.fastp.json \\
    --html ${prefix}.fastp.html \\
    $adapter_list \\
    $fail_fastq \\
    $merge_fastq \\
    --thread $task.cpus \\
    --detect_adapter_for_pe \\
    $args \\
    2> ${prefix}.fastp.log

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    fastp: \$(fastp --version 2>&1 | sed -e "s/fastp //g")
END_VERSIONS
"""
NextFlow fastp From line 78 of fastp/main.nf 
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"""
printf "%s %s\\n" $rename_to | while read old_name new_name; do
    [ -f "\${new_name}" ] || ln -s \$old_name \$new_name
done
fastqc $args --threads $task.cpus $renamed_files

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" )
END_VERSIONS
"""
NextFlow FastQC From line 28 of fastqc/main.nf 
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"""
touch ${prefix}.html
touch ${prefix}.zip

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" )
END_VERSIONS
"""
NextFlow FastQC From line 42 of fastqc/main.nf 
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"""
fq subsample \\
    $args \\
    $fastq \\
    $fastq1_output \\
    $fastq2_output

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    fq: \$(echo \$(fq subsample --version | sed 's/fq-subsample //g'))
END_VERSIONS
"""
NextFlow From line 43 of subsample/main.nf 
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"""
gffread \\
    $gff \\
    $args \\
    -o ${prefix}.gtf
cat <<-END_VERSIONS > versions.yml
"${task.process}":
    gffread: \$(gffread --version 2>&1)
END_VERSIONS
"""
NextFlow gffread From line 23 of gffread/main.nf 
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"""
gunzip \\
    -f \\
    $args \\
    $archive

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    gunzip: \$(echo \$(gunzip --version 2>&1) | sed 's/^.*(gzip) //; s/ Copyright.*\$//')
END_VERSIONS
"""
NextFlow From line 23 of gunzip/main.nf 
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"""
touch $gunzip
cat <<-END_VERSIONS > versions.yml
"${task.process}":
    gunzip: \$(echo \$(gunzip --version 2>&1) | sed 's/^.*(gzip) //; s/ Copyright.*\$//')
END_VERSIONS
"""
NextFlow From line 37 of gunzip/main.nf 
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"""
INDEX=`find -L ./ -name "*.1.ht2" | sed 's/\\.1.ht2\$//'`
hisat2 \\
    -x \$INDEX \\
    -U $reads \\
    $strandedness \\
    --known-splicesite-infile $splicesites \\
    --summary-file ${prefix}.hisat2.summary.log \\
    --threads $task.cpus \\
    $seq_center \\
    $unaligned \\
    $args \\
    | samtools view -bS -F 4 -F 256 - > ${prefix}.bam

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    hisat2: $VERSION
    samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
NextFlow SAMtools HISAT2 From line 39 of align/main.nf 
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"""
INDEX=`find -L ./ -name "*.1.ht2" | sed 's/\\.1.ht2\$//'`
hisat2 \\
    -x \$INDEX \\
    -1 ${reads[0]} \\
    -2 ${reads[1]} \\
    $strandedness \\
    --known-splicesite-infile $splicesites \\
    --summary-file ${prefix}.hisat2.summary.log \\
    --threads $task.cpus \\
    $seq_center \\
    $unaligned \\
    --no-mixed \\
    --no-discordant \\
    $args \\
    | samtools view -bS -F 4 -F 8 -F 256 - > ${prefix}.bam

if [ -f ${prefix}.unmapped.fastq.1.gz ]; then
    mv ${prefix}.unmapped.fastq.1.gz ${prefix}.unmapped_1.fastq.gz
fi
if [ -f ${prefix}.unmapped.fastq.2.gz ]; then
    mv ${prefix}.unmapped.fastq.2.gz ${prefix}.unmapped_2.fastq.gz
fi

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    hisat2: $VERSION
    samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
NextFlow SAMtools HISAT2 From line 61 of align/main.nf 
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"""
mkdir hisat2
$extract_exons
hisat2-build \\
    -p $task.cpus \\
    $ss \\
    $exon \\
    $args \\
    $fasta \\
    hisat2/${fasta.baseName}

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    hisat2: $VERSION
END_VERSIONS
"""
NextFlow HISAT2 From line 48 of build/main.nf 
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"""
hisat2_extract_splice_sites.py $gtf > ${gtf.baseName}.splice_sites.txt
cat <<-END_VERSIONS > versions.yml
"${task.process}":
    hisat2: $VERSION
END_VERSIONS
"""
NextFlow From line 24 of extractsplicesites/main.nf 
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"""
picard \\
    -Xmx${avail_mem}M \\
    MarkDuplicates \\
    $args \\
    --INPUT $bam \\
    --OUTPUT ${prefix}.bam \\
    --REFERENCE_SEQUENCE $fasta \\
    --METRICS_FILE ${prefix}.MarkDuplicates.metrics.txt

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    picard: \$(echo \$(picard MarkDuplicates --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:)
END_VERSIONS
"""
NextFlow Picard From line 33 of markduplicates/main.nf 
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"""
touch ${prefix}.bam
touch ${prefix}.bam.bai
touch ${prefix}.MarkDuplicates.metrics.txt

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    picard: \$(echo \$(picard MarkDuplicates --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:)
END_VERSIONS
"""
NextFlow From line 51 of markduplicates/main.nf 
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"""
preseq \\
    lc_extrap \\
    $args \\
    $paired_end \\
    -output ${prefix}.lc_extrap.txt \\
    $bam
cp .command.err ${prefix}.command.log

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    preseq: \$(echo \$(preseq 2>&1) | sed 's/^.*Version: //; s/Usage:.*\$//')
END_VERSIONS
"""
NextFlow preseq From line 26 of lcextrap/main.nf 
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"""
unset DISPLAY
mkdir -p tmp
export _JAVA_OPTIONS=-Djava.io.tmpdir=./tmp
qualimap \\
    --java-mem-size=$memory \\
    rnaseq \\
    $args \\
    -bam $bam \\
    -gtf $gtf \\
    -p $strandedness \\
    $paired_end \\
    -outdir $prefix

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    qualimap: \$(echo \$(qualimap 2>&1) | sed 's/^.*QualiMap v.//; s/Built.*\$//')
END_VERSIONS
"""
NextFlow QualiMap From line 33 of rnaseq/main.nf 
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"""
mkdir ${prefix}

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    qualimap: \$(echo \$(qualimap 2>&1) | sed 's/^.*QualiMap v.//; s/Built.*\$//')
END_VERSIONS
"""
NextFlow From line 55 of rnaseq/main.nf 
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"""
INDEX=`find -L ./ -name "*.grp" | sed 's/\\.grp\$//'`
rsem-calculate-expression \\
    --num-threads $task.cpus \\
    --temporary-folder ./tmp/ \\
    $strandedness \\
    $paired_end \\
    $args \\
    $reads \\
    \$INDEX \\
    $prefix

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    rsem: \$(rsem-calculate-expression --version | sed -e "s/Current version: RSEM v//g")
    star: \$(STAR --version | sed -e "s/STAR_//g")
END_VERSIONS
"""
NextFlow RSEM From line 39 of calculateexpression/main.nf 
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"""
STAR \\
    --runMode genomeGenerate \\
    --genomeDir rsem/ \\
    --genomeFastaFiles $fasta \\
    --sjdbGTFfile $gtf \\
    --runThreadN $task.cpus \\
    $memory \\
    $args2

rsem-prepare-reference \\
    --gtf $gtf \\
    --num-threads $task.cpus \\
    ${args_list.join(' ')} \\
    $fasta \\
    rsem/genome

cp rsem/genome.transcripts.fa .

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    rsem: \$(rsem-calculate-expression --version | sed -e "s/Current version: RSEM v//g")
    star: \$(STAR --version | sed -e "s/STAR_//g")
END_VERSIONS
"""
NextFlow STAR RSEM From line 29 of preparereference/main.nf 
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"""
rsem-prepare-reference \\
    --gtf $gtf \\
    --num-threads $task.cpus \\
    $args \\
    $fasta \\
    rsem/genome

cp rsem/genome.transcripts.fa .

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    rsem: \$(rsem-calculate-expression --version | sed -e "s/Current version: RSEM v//g")
    star: \$(STAR --version | sed -e "s/STAR_//g")
END_VERSIONS
"""
NextFlow RSEM From line 55 of preparereference/main.nf 
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"""
bam_stat.py \\
    -i $bam \\
    $args \\
    > ${prefix}.bam_stat.txt

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    rseqc: \$(bam_stat.py --version | sed -e "s/bam_stat.py //g")
END_VERSIONS
"""
NextFlow From line 23 of bamstat/main.nf 
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"""
infer_experiment.py \\
    -i $bam \\
    -r $bed \\
    $args \\
    > ${prefix}.infer_experiment.txt

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    rseqc: \$(infer_experiment.py --version | sed -e "s/infer_experiment.py //g")
END_VERSIONS
"""
NextFlow From line 24 of inferexperiment/main.nf 
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"""
inner_distance.py \\
    -i $bam \\
    -r $bed \\
    -o $prefix \\
    $args \\
    > stdout.txt
head -n 2 stdout.txt > ${prefix}.inner_distance_mean.txt

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    rseqc: \$(inner_distance.py --version | sed -e "s/inner_distance.py //g")
END_VERSIONS
"""
NextFlow From line 29 of innerdistance/main.nf 
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"""
cat <<-END_VERSIONS > versions.yml
"${task.process}":
    rseqc: \$(inner_distance.py --version | sed -e "s/inner_distance.py //g")
END_VERSIONS
"""
NextFlow From line 44 of innerdistance/main.nf 
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"""
junction_annotation.py \\
    -i $bam \\
    -r $bed \\
    -o $prefix \\
    $args \\
    2> ${prefix}.junction_annotation.log

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    rseqc: \$(junction_annotation.py --version | sed -e "s/junction_annotation.py //g")
END_VERSIONS
"""
NextFlow From line 30 of junctionannotation/main.nf 
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"""
junction_saturation.py \\
    -i $bam \\
    -r $bed \\
    -o $prefix \\
    $args

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    rseqc: \$(junction_saturation.py --version | sed -e "s/junction_saturation.py //g")
END_VERSIONS
"""
NextFlow From line 25 of junctionsaturation/main.nf 
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"""
read_distribution.py \\
    -i $bam \\
    -r $bed \\
    > ${prefix}.read_distribution.txt

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    rseqc: \$(read_distribution.py --version | sed -e "s/read_distribution.py //g")
END_VERSIONS
"""
NextFlow From line 24 of readdistribution/main.nf 
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"""
read_duplication.py \\
    -i $bam \\
    -o $prefix \\
    $args

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    rseqc: \$(read_duplication.py --version | sed -e "s/read_duplication.py //g")
END_VERSIONS
"""
NextFlow From line 26 of readduplication/main.nf 
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"""
tin.py \\
    -i $bam \\
    -r $bed \\
    $args

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    rseqc: \$(tin.py --version | sed -e "s/tin.py //g")
END_VERSIONS
"""
NextFlow From line 25 of tin/main.nf 
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"""
$get_decoy_ids
sed -i.bak -e 's/>//g' decoys.txt
cat $transcript_fasta $genome_fasta > $gentrome

salmon \\
    index \\
    --threads $task.cpus \\
    -t $gentrome \\
    -d decoys.txt \\
    $args \\
    -i salmon

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    salmon: \$(echo \$(salmon --version) | sed -e "s/salmon //g")
END_VERSIONS
"""
NextFlow Salmon From line 29 of index/main.nf 
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"""
salmon quant \\
    --geneMap $gtf \\
    --threads $task.cpus \\
    --libType=$strandedness \\
    $reference \\
    $input_reads \\
    $args \\
    -o $prefix

if [ -f $prefix/aux_info/meta_info.json ]; then
    cp $prefix/aux_info/meta_info.json "${prefix}_meta_info.json"
fi

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    salmon: \$(echo \$(salmon --version) | sed -e "s/salmon //g")
END_VERSIONS
"""
NextFlow Quant Salmon From line 58 of quant/main.nf 
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"""
samtools \\
    flagstat \\
    --threads ${task.cpus} \\
    $bam \\
    > ${prefix}.flagstat

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
NextFlow SAMtools From line 23 of flagstat/main.nf 
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"""
samtools \\
    idxstats \\
    --threads ${task.cpus-1} \\
    $bam \\
    > ${prefix}.idxstats

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
NextFlow SAMtools From line 24 of idxstats/main.nf 
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"""
samtools \\
    index \\
    -@ ${task.cpus-1} \\
    $args \\
    $input

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
NextFlow SAMtools From line 24 of index/main.nf 
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"""
touch ${input}.bai
touch ${input}.crai
touch ${input}.csi

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
NextFlow From line 38 of index/main.nf 
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"""
samtools sort \\
    $args \\
    -@ $task.cpus \\
    -o ${prefix}.bam \\
    -T $prefix \\
    $bam

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
NextFlow SAMtools From line 25 of sort/main.nf 
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"""
touch ${prefix}.bam

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
NextFlow From line 41 of sort/main.nf 
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"""
samtools \\
    stats \\
    --threads ${task.cpus} \\
    ${reference} \\
    ${input} \\
    > ${prefix}.stats

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
NextFlow SAMtools From line 25 of stats/main.nf 
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"""
touch ${prefix}.stats

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
NextFlow From line 41 of stats/main.nf 
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"""
sortmerna \\
    ${'--ref '+fastas.join(' --ref ')} \\
    --reads $reads \\
    --threads $task.cpus \\
    --workdir . \\
    --aligned rRNA_reads \\
    --fastx \\
    --other non_rRNA_reads \\
    $args

mv non_rRNA_reads.f*q.gz ${prefix}.non_rRNA.fastq.gz
mv rRNA_reads.log ${prefix}.sortmerna.log

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    sortmerna: \$(echo \$(sortmerna --version 2>&1) | sed 's/^.*SortMeRNA version //; s/ Build Date.*\$//')
END_VERSIONS
"""
NextFlow From line 26 of sortmerna/main.nf 
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"""
sortmerna \\
    ${'--ref '+fastas.join(' --ref ')} \\
    --reads ${reads[0]} \\
    --reads ${reads[1]} \\
    --threads $task.cpus \\
    --workdir . \\
    --aligned rRNA_reads \\
    --fastx \\
    --other non_rRNA_reads \\
    --paired_in \\
    --out2 \\
    $args

mv non_rRNA_reads_fwd.f*q.gz ${prefix}_1.non_rRNA.fastq.gz
mv non_rRNA_reads_rev.f*q.gz ${prefix}_2.non_rRNA.fastq.gz
mv rRNA_reads.log ${prefix}.sortmerna.log

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    sortmerna: \$(echo \$(sortmerna --version 2>&1) | sed 's/^.*SortMeRNA version //; s/ Build Date.*\$//')
END_VERSIONS
"""
NextFlow From line 46 of sortmerna/main.nf 
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"""
STAR \\
    --genomeDir $index \\
    --readFilesIn ${reads1.join(",")} ${reads2.join(",")} \\
    --runThreadN $task.cpus \\
    --outFileNamePrefix $prefix. \\
    $out_sam_type \\
    $ignore_gtf \\
    $attrRG \\
    $args

$mv_unsorted_bam

if [ -f ${prefix}.Unmapped.out.mate1 ]; then
    mv ${prefix}.Unmapped.out.mate1 ${prefix}.unmapped_1.fastq
    gzip ${prefix}.unmapped_1.fastq
fi
if [ -f ${prefix}.Unmapped.out.mate2 ]; then
    mv ${prefix}.Unmapped.out.mate2 ${prefix}.unmapped_2.fastq
    gzip ${prefix}.unmapped_2.fastq
fi

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    star: \$(STAR --version | sed -e "s/STAR_//g")
    samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
    gawk: \$(echo \$(gawk --version 2>&1) | sed 's/^.*GNU Awk //; s/, .*\$//')
END_VERSIONS
"""
NextFlow STAR From line 51 of align/main.nf 
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"""
touch ${prefix}Xd.out.bam
touch ${prefix}.Log.final.out
touch ${prefix}.Log.out
touch ${prefix}.Log.progress.out
touch ${prefix}.sortedByCoord.out.bam
touch ${prefix}.toTranscriptome.out.bam
touch ${prefix}.Aligned.unsort.out.bam
touch ${prefix}.Aligned.sortedByCoord.out.bam
touch ${prefix}.unmapped_1.fastq.gz
touch ${prefix}.unmapped_2.fastq.gz
touch ${prefix}.tab
touch ${prefix}.SJ.out.tab
touch ${prefix}.ReadsPerGene.out.tab
touch ${prefix}.Chimeric.out.junction
touch ${prefix}.out.sam
touch ${prefix}.Signal.UniqueMultiple.str1.out.wig
touch ${prefix}.Signal.UniqueMultiple.str1.out.bg

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    star: \$(STAR --version | sed -e "s/STAR_//g")
    samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
    gawk: \$(echo \$(gawk --version 2>&1) | sed 's/^.*GNU Awk //; s/, .*\$//')
END_VERSIONS
"""
NextFlow From line 83 of align/main.nf 
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"""
mkdir star
STAR \\
    --runMode genomeGenerate \\
    --genomeDir star/ \\
    --genomeFastaFiles $fasta \\
    --sjdbGTFfile $gtf \\
    --runThreadN $task.cpus \\
    $memory \\
    $args

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    star: \$(STAR --version | sed -e "s/STAR_//g")
    samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
    gawk: \$(echo \$(gawk --version 2>&1) | sed 's/^.*GNU Awk //; s/, .*\$//')
END_VERSIONS
"""
NextFlow STAR From line 26 of genomegenerate/main.nf 
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"""
samtools faidx $fasta
NUM_BASES=`gawk '{sum = sum + \$2}END{if ((log(sum)/log(2))/2 - 1 > 14) {printf "%.0f", 14} else {printf "%.0f", (log(sum)/log(2))/2 - 1}}' ${fasta}.fai`

mkdir star
STAR \\
    --runMode genomeGenerate \\
    --genomeDir star/ \\
    --genomeFastaFiles $fasta \\
    --sjdbGTFfile $gtf \\
    --runThreadN $task.cpus \\
    --genomeSAindexNbases \$NUM_BASES \\
    $memory \\
    $args

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    star: \$(STAR --version | sed -e "s/STAR_//g")
    samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
    gawk: \$(echo \$(gawk --version 2>&1) | sed 's/^.*GNU Awk //; s/, .*\$//')
END_VERSIONS
"""
NextFlow SAMtools STAR From line 45 of genomegenerate/main.nf 
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"""
mkdir star
touch star/Genome
touch star/Log.out
touch star/SA
touch star/SAindex
touch star/chrLength.txt
touch star/chrName.txt
touch star/chrNameLength.txt
touch star/chrStart.txt
touch star/exonGeTrInfo.tab
touch star/exonInfo.tab
touch star/geneInfo.tab
touch star/genomeParameters.txt
touch star/sjdbInfo.txt
touch star/sjdbList.fromGTF.out.tab
touch star/sjdbList.out.tab
touch star/transcriptInfo.tab

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    star: \$(STAR --version | sed -e "s/STAR_//g")
    samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
    gawk: \$(echo \$(gawk --version 2>&1) | sed 's/^.*GNU Awk //; s/, .*\$//')
END_VERSIONS
"""
NextFlow From line 70 of genomegenerate/main.nf 
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"""
stringtie \\
    $bam \\
    $strandedness \\
    $reference \\
    -o ${prefix}.transcripts.gtf \\
    -A ${prefix}.gene.abundance.txt \\
    $coverage \\
    $ballgown \\
    -p $task.cpus \\
    $args

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    stringtie: \$(stringtie --version 2>&1)
END_VERSIONS
"""
NextFlow StringTie From line 37 of stringtie/main.nf 
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"""
touch ${prefix}.transcripts.gtf
touch ${prefix}.gene.abundance.txt
touch ${prefix}.coverage.gtf
touch ${prefix}.ballgown

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    stringtie: \$(stringtie --version 2>&1)
END_VERSIONS
"""
NextFlow From line 57 of stringtie/main.nf 
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"""
featureCounts \\
    $args \\
    $paired_end \\
    -T $task.cpus \\
    -a $annotation \\
    -s $strandedness \\
    -o ${prefix}.featureCounts.txt \\
    ${bams.join(' ')}

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    subread: \$( echo \$(featureCounts -v 2>&1) | sed -e "s/featureCounts v//g")
END_VERSIONS
"""
NextFlow FeatureCounts From line 32 of featurecounts/main.nf 
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"""
[ ! -f  ${prefix}.fastq.gz ] && ln -s $reads ${prefix}.fastq.gz
trim_galore \\
    ${args_list.join(' ')} \\
    --cores $cores \\
    --gzip \\
    ${prefix}.fastq.gz

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    trimgalore: \$(echo \$(trim_galore --version 2>&1) | sed 's/^.*version //; s/Last.*\$//')
    cutadapt: \$(cutadapt --version)
END_VERSIONS
"""
NextFlow Trim_Galore From line 42 of trimgalore/main.nf 
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"""
[ ! -f  ${prefix}_1.fastq.gz ] && ln -s ${reads[0]} ${prefix}_1.fastq.gz
[ ! -f  ${prefix}_2.fastq.gz ] && ln -s ${reads[1]} ${prefix}_2.fastq.gz
trim_galore \\
    $args \\
    --cores $cores \\
    --paired \\
    --gzip \\
    ${prefix}_1.fastq.gz \\
    ${prefix}_2.fastq.gz

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    trimgalore: \$(echo \$(trim_galore --version 2>&1) | sed 's/^.*version //; s/Last.*\$//')
    cutadapt: \$(cutadapt --version)
END_VERSIONS
"""
NextFlow Trim_Galore From line 57 of trimgalore/main.nf 
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"""
bedClip \\
    $bedgraph \\
    $sizes \\
    ${prefix}.bedGraph

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    ucsc: $VERSION
END_VERSIONS
"""
NextFlow ucsc-bedclip From line 26 of bedclip/main.nf 
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"""
bedGraphToBigWig \\
    $bedgraph \\
    $sizes \\
    ${prefix}.bigWig

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    ucsc: $VERSION
END_VERSIONS
"""
NextFlow bedGraphToBigWig From line 26 of bedgraphtobigwig/main.nf 
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"""
PYTHONHASHSEED=0 umi_tools \\
    dedup \\
    -I $bam \\
    -S ${prefix}.bam \\
    $stats \\
    $paired \\
    $args

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    umitools: \$(umi_tools --version 2>&1 | sed 's/^.*UMI-tools version://; s/ *\$//')
END_VERSIONS
"""
NextFlow umi_tools From line 31 of dedup/main.nf 
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"""
umi_tools \\
    extract \\
    -I $reads \\
    -S ${prefix}.umi_extract.fastq.gz \\
    $args \\
    > ${prefix}.umi_extract.log

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    umitools: \$(umi_tools --version 2>&1 | sed 's/^.*UMI-tools version://; s/ *\$//')
END_VERSIONS
"""
NextFlow umi_tools From line 26 of extract/main.nf 
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"""
umi_tools \\
    extract \\
    -I ${reads[0]} \\
    --read2-in=${reads[1]} \\
    -S ${prefix}.umi_extract_1.fastq.gz \\
    --read2-out=${prefix}.umi_extract_2.fastq.gz \\
    $args \\
    > ${prefix}.umi_extract.log

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    umitools: \$(umi_tools --version 2>&1 | sed 's/^.*UMI-tools version://; s/ *\$//')
END_VERSIONS
"""
NextFlow umi_tools From line 40 of extract/main.nf 
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"""
mkdir $prefix

## Ensures --strip-components only applied when top level of tar contents is a directory
## If just files or multiple directories, place all in prefix
if [[ \$(tar -taf ${archive} | grep -o -P "^.*?\\/" | uniq | wc -l) -eq 1 ]]; then
    tar \\
        -C $prefix --strip-components 1 \\
        -xavf \\
        $args \\
        $archive \\
        $args2
else
    tar \\
        -C $prefix \\
        -xavf \\
        $args \\
        $archive \\
        $args2
fi

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    untar: \$(echo \$(tar --version 2>&1) | sed 's/^.*(GNU tar) //; s/ Copyright.*\$//')
END_VERSIONS
"""
NextFlow From line 25 of untar/main.nf 
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"""
mkdir $prefix
touch ${prefix}/file.txt

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    untar: \$(echo \$(tar --version 2>&1) | sed 's/^.*(GNU tar) //; s/ Copyright.*\$//')
END_VERSIONS
"""
NextFlow From line 54 of untar/main.nf
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Created: 1yr ago
Updated: 1yr ago
Maitainers: public
URL: https://github.com/nf-core/rnaseq
Name: nf-core-rnaseq
Version: Version 1
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