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Merge pull request #1 from grp-bork/update/nevermore_0.13.0_20240620
Update/nevermore 0.13.0 20240620
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,76 @@ | ||
| process bowtie2_build { | ||
| container "quay.io/biocontainers/bowtie2:2.5.3--py39h6fed5c7_1" | ||
| tag "${sample.id}" | ||
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| input: | ||
| tuple val(sample), path(genomeseq) | ||
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| output: | ||
| tuple val(sample), path("${sample.id}/bowtie2/${sample.id}*"), emit: index | ||
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| script: | ||
| """ | ||
| mkdir -p ${sample.id}/bowtie2/ | ||
| gzip -dc ${genomeseq} > genome.fa | ||
| bowtie2-build --threads ${task.cpus} -f genome.fa ${sample.id}/bowtie2/${sample.id} | ||
| rm -vf genome.fa | ||
| """ | ||
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| } | ||
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| process bowtie2_align { | ||
| // container "quay.io/biocontainers/bowtie2:2.5.3--py39h6fed5c7_1" | ||
| container "registry.git.embl.de/schudoma/bowtie2-docker:latest" | ||
| tag "${sample.id}" | ||
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| input: | ||
| tuple val(sample), path(fastqs), path(index) | ||
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| output: | ||
| tuple val(sample), path("${sample.id}/bowtie2_align/${sample.id}.bam"), emit: bam | ||
| tuple val(sample), path("${sample.id}/bowtie2_align/${sample.id}.bam.bai"), emit: bai | ||
| tuple val(sample), path("${sample.id}.BOWTIE2.DONE"), emit: sentinel | ||
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| script: | ||
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| def input_files = "" | ||
| def r1_files = fastqs.findAll( { it.name.endsWith("_R1.fastq.gz") && !it.name.matches("(.*)(singles|orphans|chimeras)(.*)") } ) | ||
| def r2_files = fastqs.findAll( { it.name.endsWith("_R2.fastq.gz") } ) | ||
| def orphans = fastqs.findAll( { it.name.matches("(.*)(singles|orphans|chimeras)(.*)") } ) | ||
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| if (r1_files.size() != 0 && r2_files.size() != 0) { | ||
| input_files += "-1 ${r1_files.join(' ')} -2 ${r2_files.join(' ')}" | ||
| single_reads = false | ||
| } else if (r1_files.size() != 0) { | ||
| input_files += "-U ${r1_files.join(' ')}" | ||
| } else if (r2_files.size() != 0) { | ||
| input_files += "-U ${r2_files.join(' ')}" | ||
| } else if (orphans.size() != 0) { | ||
| input_files += "-U ${orphans.join(' ')}" | ||
| } | ||
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| // --fr/--rf/--ff | ||
| def threads = task.cpus.intdiv(2) | ||
| def bowtie2_options = "-p ${threads} -q --phred33" | ||
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| def index_id = index[0].name.replaceAll(/.[0-9]+.bt2[l]?$/, "") | ||
| // -S ${sample.id}/hisat2_align/${sample.id}.sam | ||
| // index_id=\$(ls ${index[0]} | sed 's/\\.[0-9]\\+\\.ht2\$//') | ||
| """ | ||
| mkdir -p ${sample.id}/bowtie2_align/ tmp/ | ||
| export TMPDIR=tmp/ | ||
| bowtie2 -x ${index_id} ${bowtie2_options} ${input_files} > ${sample.id}.sam | ||
| samtools sort -@ ${threads} ${sample.id}.sam > ${sample.id}/bowtie2_align/${sample.id}.bam | ||
| samtools index ${sample.id}/bowtie2_align/${sample.id}.bam | ||
| rm -fv ${sample.id}.sam | ||
| touch ${sample.id}.BOWTIE2.DONE | ||
| """ | ||
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||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,86 @@ | ||
| process hisat2_build { | ||
| container "quay.io/biocontainers/hisat2:2.2.1--hdbdd923_6" | ||
| // we need a hisat2/samtools mixed container | ||
| // container "registry.git.embl.de/schudoma/hisat2-docker:latest" | ||
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| input: | ||
| tuple val(sample), path(genomeseq) | ||
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| output: | ||
| tuple val(sample), path("${sample.id}/hisat2/${sample.id}*"), emit: index | ||
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| script: | ||
| """ | ||
| mkdir -p ${sample.id}/hisat2/ | ||
| gzip -dc ${genomeseq} > genome.fa | ||
| hisat2-build -f genome.fa ${sample.id}/hisat2/${sample.id} | ||
| rm -vf genome.fa | ||
| """ | ||
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| } | ||
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| process hisat2_align { | ||
| // container "quay.io/biocontainers/hisat2:2.2.1--hdbdd923_6" | ||
| // we need a hisat2/samtools mixed container | ||
| container "registry.git.embl.de/schudoma/hisat2-docker:latest" | ||
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| input: | ||
| tuple val(sample), path(fastqs), path(index) | ||
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| output: | ||
| // tuple val(sample), path("${sample.id}/hisat2_align/${sample.id}.bam"), path("${sample.id}/hisat2_align/${sample.id}.bam.bai"), emit: bam | ||
| tuple val(sample), path("${sample.id}/hisat2_align/${sample.id}.bam"), emit: bam | ||
| tuple val(sample), path("${sample.id}/hisat2_align/${sample.id}.bam.bai"), emit: bai | ||
| tuple val(sample), path("${sample.id}.HISAT2.DONE"), emit: sentinel | ||
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| script: | ||
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| def input_files = "" | ||
| def r1_files = fastqs.findAll( { it.name.endsWith("_R1.fastq.gz") && !it.name.matches("(.*)(singles|orphans|chimeras)(.*)") } ) | ||
| def r2_files = fastqs.findAll( { it.name.endsWith("_R2.fastq.gz") } ) | ||
| def orphans = fastqs.findAll( { it.name.matches("(.*)(singles|orphans|chimeras)(.*)") } ) | ||
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| if (r1_files.size() != 0 && r2_files.size() != 0) { | ||
| input_files += "-1 ${r1_files.join(' ')} -2 ${r2_files.join(' ')}" | ||
| single_reads = false | ||
| } else if (r1_files.size() != 0) { | ||
| input_files += "-U ${r1_files.join(' ')}" | ||
| } else if (r2_files.size() != 0) { | ||
| input_files += "-U ${r2_files.join(' ')}" | ||
| } else if (orphans.size() != 0) { | ||
| input_files += "-U ${orphans.join(' ')}" | ||
| } | ||
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| // --fr/--rf/--ff | ||
| def threads = task.cpus.intdiv(2) | ||
| def hisat2_options = "-p ${threads} -q --phred33" | ||
| if (params.hisat2_no_spliced_alignment) { | ||
| // --no-spliced-alignment | ||
| hisat2_options += " --no-spliced-alignment" | ||
| } | ||
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| def index_id = index[0].name.replaceAll(/.[0-9]+.ht2$/, "") | ||
| // -S ${sample.id}/hisat2_align/${sample.id}.sam | ||
| // index_id=\$(ls ${index[0]} | sed 's/\\.[0-9]\\+\\.ht2\$//') | ||
| """ | ||
| mkdir -p ${sample.id}/hisat2_align/ tmp/ | ||
| export TMPDIR=tmp/ | ||
| hisat2 -x ${index_id} ${hisat2_options} ${input_files} > ${sample.id}.sam | ||
| samtools sort -@ ${threads} ${sample.id}.sam > ${sample.id}/hisat2_align/${sample.id}.bam | ||
| samtools index ${sample.id}/hisat2_align/${sample.id}.bam | ||
| rm -fv ${sample.id}.sam | ||
| touch ${sample.id}.HISAT2.DONE | ||
| """ | ||
| // echo "tmpdir is \$TMPDIR" | ||
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| // hisat2 -x ${sample.id} ${hisat2_options} ${input_files} > ${sample.id}.sam | ||
| } | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,50 @@ | ||
| process minimap2_align { | ||
| container "registry.git.embl.de/schudoma/minimap2-docker:latest" | ||
| label 'align' | ||
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| input: | ||
| tuple val(sample), path(fastqs) | ||
| path(reference) | ||
| val(do_name_sort) | ||
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| output: | ||
| tuple val(sample), path("${sample.id}/${sample.id}.sam"), emit: sam | ||
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| script: | ||
| // def reads = (sample.is_paired) ? "${sample.id}_R1.fastq.gz ${sample.id}_R2.fastq.gz" : "${sample.id}_R1.fastq.gz" | ||
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| def input_files = "" | ||
| def r1_files = fastqs.findAll( { it.name.endsWith("_R1.fastq.gz") && !it.name.matches("(.*)(singles|orphans|chimeras)(.*)") } ) | ||
| def r2_files = fastqs.findAll( { it.name.endsWith("_R2.fastq.gz") } ) | ||
| def orphans = fastqs.findAll( { it.name.matches("(.*)(singles|orphans|chimeras)(.*)") } ) | ||
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| if (r1_files.size() != 0 && r2_files.size() != 0) { | ||
| input_files += "${r1_files.join(' ')} ${r2_files.join(' ')}" | ||
| single_reads = false | ||
| } else if (r1_files.size() != 0) { | ||
| input_files += "${r1_files.join(' ')}" | ||
| } else if (r2_files.size() != 0) { | ||
| input_files += "${r2_files.join(' ')}" | ||
| } else if (orphans.size() != 0) { | ||
| input_files += "${orphans.join(' ')}" | ||
| } | ||
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| def threads = task.cpus.intdiv(2) | ||
| // def mm_options = "--sam-hit-only -t ${threads} -x sr --secondary=yes -a" | ||
| def mm_options = "-t ${threads} -x sr --secondary=yes -a" | ||
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| // def sort_cmd = "| " + ((do_name_sort) ? "samtools collate -@ ${threads} -o ${sample.id}.bam - tmp/collated_bam" : "samtools sort -@ ${threads} -o ${sample.id}.bam -") | ||
| def sort_cmd = "" // we cannot convert large catalogue alignments to bam, hence we cannot properly sort those | ||
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| """ | ||
| set -e -o pipefail | ||
| mkdir -p ${sample.id}/ tmp/ | ||
| minimap2 ${mm_options} --split-prefix ${sample.id}_split ${reference} ${input_files} ${sort_cmd} > ${sample.id}/${sample.id}.sam | ||
| rm -rvf tmp/ | ||
| """ | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,4 +1,6 @@ | ||
| process collate_stats { | ||
| label "default" | ||
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| input: | ||
| path(stats_files) | ||
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