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Merge pull request #61 from UMCUGenetics/release/v0.5.0
Release v0.5.0
2 parents 94c4027 + 109e832 commit a2f6cc8

11 files changed

Lines changed: 112 additions & 11 deletions

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‎Fastp/0.14.1/Fastp.nf‎

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@@ -13,7 +13,7 @@ process Fastp {
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script:
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//adapted from https://github.com/nf-core/eager/blob/master/LICENSE, Copyright (c) Alexander Peltzer, Stephen Clayton, James A. Fellows Yates, Maxime Borry
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if (params.singleEnd) {
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if (params.single_end) {
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"""
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fastp --in1 ${fastq_files[0]} --out1 "${fastq_files[0].simpleName}.trim.fastq.gz" -j ${sample_id}_fastp.json ${params.optional}
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"""

‎Fastp/0.20.1/Fastp.nf‎

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Original file line numberDiff line numberDiff line change
@@ -13,7 +13,7 @@ process Fastp {
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script:
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//adapted from https://github.com/nf-core/eager/blob/master/LICENSE, Copyright (c) Alexander Peltzer, Stephen Clayton, James A. Fellows Yates, Maxime Borry
16-
if (params.singleEnd) {
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if (params.single_end) {
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"""
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fastp --in1 ${fastq_files[0]} --out1 "${fastq_files[0].simpleName}_trim.fastq.gz" -j ${sample_id}_fastp.json ${params.optional}
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"""

‎Pandocker/21.02/MarkdownToPdf.nf‎

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@@ -0,0 +1,24 @@
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process MarkdownToPdf {
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tag {"Pandocker MarkdownToPdf"}
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label 'Pandocker_21_02'
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label 'Pandocker_21_02_MarkdownToPdf'
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container = 'library://dalibo/pandocker:v21.02'
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shell = ['/bin/bash', '-euo', 'pipefail']
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input:
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path(md_file)
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output:
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path("${md_file.baseName}.pdf")
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script:
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"""
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pandoc ${md_file} \
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--variable urlcolor=blue \
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-s \
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--toc \
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-f markdown \
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-o ${md_file.baseName}.pdf
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"""
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}

‎STARFusion/1.8.1/STARFusion.nf‎

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Original file line numberDiff line numberDiff line change
@@ -17,7 +17,7 @@ process STARFusion {
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script:
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//Adapted code from: https://github.com/nf-core/rnafusion - MIT License - Copyright (c) Martin Proks
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def avail_mem = task.memory ? "--limitGenomeGenerateRAM ${task.memory.toBytes() - 100000000}" : ''
20-
def read_args = params.singleEnd ? "--left_fq ${fastq_files[0]}" : "--left_fq ${fastq_files[0]} --right_fq ${fastq_files[1]}"
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def read_args = params.single_end ? "--left_fq ${fastq_files[0]}" : "--left_fq ${fastq_files[0]} --right_fq ${fastq_files[1]}"
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"""
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STAR \
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--genomeDir ${star_index} \

‎Salmon/1.2.1/Quant.nf‎

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -14,13 +14,13 @@ process Quant {
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script:
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//Adapted code from: https://github.com/nf-core/rnaseq - MIT License - Copyright (c) Phil Ewels, Rickard Hammarén
17-
def rnastrandness = params.singleEnd ? 'U' : 'IU'
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def rnastrandness = params.single_end ? 'U' : 'IU'
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if (params.stranded && !params.unstranded) {
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rnastrandness = params.singleEnd ? 'SF' : 'ISF'
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rnastrandness = params.single_end ? 'SF' : 'ISF'
2020
} else if (params.revstranded && !params.unstranded) {
21-
rnastrandness = params.singleEnd ? 'SR' : 'ISR'
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rnastrandness = params.single_end ? 'SR' : 'ISR'
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}
23-
def endedness = params.singleEnd ? "-r ${fastq_files[0]}" : "-1 ${fastq_files[0]} -2 ${fastq_files[1]}"
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def endedness = params.single_end ? "-r ${fastq_files[0]}" : "-1 ${fastq_files[0]} -2 ${fastq_files[1]}"
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def unmapped = params.saveUnaligned ? "--writeUnmappedNames" : ''
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"""

‎SortMeRNA/4.2.0/SortMeRNA.nf‎

Lines changed: 7 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -17,7 +17,7 @@ process SortMeRNA {
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script:
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def Refs = db_fasta.collect{ "$it" }.join(" -ref ")
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def report_title = fastq_files[0].simpleName.split("_R1_")[0]
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if (params.singleEnd) {
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if (params.single_end) {
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"""
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sortmerna -ref ${Refs} \
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-reads ${fastq_files} \
@@ -31,6 +31,8 @@ process SortMeRNA {
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gzip -f < non-rRNA-reads.fastq > ${fastq_files[0].simpleName}_non_rRNA.fastq.gz
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gzip -f < rRNA-reads.fastq > ${fastq_files[0].simpleName}_filtered_rRNA.fastq.gz
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mv rRNA-reads.log ${report_title}_rRNA_report.txt
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rm non-rRNA-reads.fastq
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rm rRNA-reads.fastq
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"""
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} else {
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"""
@@ -49,6 +51,10 @@ process SortMeRNA {
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gzip < rRNA-reads_fwd.fastq > ${fastq_files[0].simpleName}_filtered_rRNA.fastq.gz
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gzip < rRNA-reads_rev.fastq > ${fastq_files[1].simpleName}_filtered_rRNA.fastq.gz
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mv rRNA-reads.log ${report_title}_rRNA_report.txt
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rm non-rRNA-reads_fwd.fastq
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rm non-rRNA-reads_rev.fastq
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rm rRNA-reads_fwd.fastq
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rm rRNA-reads_rev.fastq
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"""
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}
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}

‎SortMeRNA/4.3.3/SortMeRNA.nf‎

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Original file line numberDiff line numberDiff line change
@@ -0,0 +1,55 @@
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process SortMeRNA {
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tag {"SortMeRNA ${sample_id}"}
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label 'SortMeRNA_4_3_3'
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container = 'quay.io/biocontainers/sortmerna:4.3.3--h9ee0642_0'
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shell = ['/bin/bash', '-euo', 'pipefail']
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input:
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tuple(sample_id, rg_id, path(fastq_files))
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path(db_fasta)
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output:
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tuple(sample_id, rg_id, path("*_non_rRNA.fastq.gz"), emit: non_rRNA_fastqs)
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path("*_filtered_rRNA.fastq.gz", emit: rRNA_fastqs)
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path("*_rRNA_report.txt", emit: qc_report)
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script:
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def refs = db_fasta.collect{ "$it" }.join(" -ref ")
18+
def report_title = fastq_files[0].simpleName.split("_R1_")[0]
19+
if (params.single_end) {
20+
"""
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sortmerna -ref ${refs} \
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-reads ${fastq_files} \
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--num_alignments 1 \
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--threads ${task.cpus} \
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--fastx \
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-workdir \${PWD} \
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--aligned rRNA-reads \
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--other non-rRNA-reads \
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--zip-out
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mv non-rRNA-reads.fq.gz ${fastq_files[0].simpleName}_non_rRNA.fastq.gz
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mv rRNA-reads.fq.gz ${fastq_files[0].simpleName}_filtered_rRNA.fastq.gz
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mv rRNA-reads.log ${report_title}_rRNA_report.txt
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"""
35+
} else {
36+
"""
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sortmerna -ref ${refs} \
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-reads ${fastq_files[0]} -reads ${fastq_files[1]} \
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--num_alignments 1 \
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--threads ${task.cpus} \
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-workdir \${PWD} \
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--fastx -paired_in \
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--aligned rRNA-reads \
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--other non-rRNA-reads \
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-out2 \
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--zip-out
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48+
mv non-rRNA-reads_fwd.fq.gz ${fastq_files[0].simpleName}_non_rRNA.fastq.gz
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mv non-rRNA-reads_rev.fq.gz ${fastq_files[1].simpleName}_non_rRNA.fastq.gz
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mv rRNA-reads_fwd.fq.gz ${fastq_files[0].simpleName}_filtered_rRNA.fastq.gz
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mv rRNA-reads_rev.fq.gz ${fastq_files[1].simpleName}_filtered_rRNA.fastq.gz
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mv rRNA-reads.log ${report_title}_rRNA_report.txt
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"""
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}
55+
}

‎Subread/2.0.0/FeatureCounts.nf‎

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Original file line numberDiff line numberDiff line change
@@ -21,7 +21,7 @@ process FeatureCounts {
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def bam_list = bam_file.collect{ "$it" }.join(" ")
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def biotype = params.gencode ? "gene_type" : params.fc_group_features_type
2323
def extraAttributes = params.fc_extra_attributes ? "--extraAttributes ${params.fc_extra_attributes}" : ''
24-
def fragment_mode = !params.singleEnd ? "-p": ''
24+
def fragment_mode = !params.single_end ? "-p": ''
2525
//Get strandedness
2626
def featureCounts_direction = 0
2727
if (params.stranded && !params.unstranded) {

‎TrimGalore/0.6.5/TrimGalore.nf‎

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Original file line numberDiff line numberDiff line change
@@ -13,7 +13,7 @@ process TrimGalore {
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path("*_fastqc.{zip,html}", optional: true, emit: fastqc_report)
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script:
16-
if (params.singleEnd) {
16+
if (params.single_end) {
1717
"""
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trim_galore ${fastq_files} --gzip ${params.optional}
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mv ${fastq_files[0].simpleName}_trimmed.fq.gz ${fastq_files[0].simpleName}_trimmed.fastq.gz

‎Utils/MergeFastqLanes.nf‎

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Original file line numberDiff line numberDiff line change
@@ -14,7 +14,7 @@ process MergeFastqLanes {
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barcode = rg_id.split('_')[1]
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def R1_pattern="${sample_id}_*_S*_L00*_R1_001*.fastq.gz"
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def R2_pattern="${sample_id}_*_S*_L00*_R2_001*.fastq.gz"
17-
if (params.singleEnd) {
17+
if (params.single_end) {
1818
"""
1919
cat \$( ls ${R1_pattern} | sort | paste \$(printf "%0.s- " \$(seq 1 \$( ls ${R1_pattern} | wc -l)))) > ${sample_id}_${barcode}_merged_R1.fastq.gz
2020
"""

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