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Merge branch 'single-read-raw-clean' into single-read-profile
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,34 +1,38 @@ | ||
| // Truncate concatenated read files for trial run | ||
| process TRUNCATE_CONCAT { | ||
| process TRUNCATE_CONCAT_PAIRED { | ||
| label "single" | ||
| label "BBTools" | ||
| input: | ||
| tuple val(sample), path(reads) | ||
| val n_reads | ||
| val single_end | ||
| output: | ||
|
|
||
| tuple val(sample), path({ | ||
| single_end ? | ||
| "${sample}_trunc.fastq.gz" : | ||
| "${sample}_trunc_{1,2}.fastq.gz" | ||
| }), emit: reads | ||
| tuple val(sample), path("${sample}_trunc_{1,2}.fastq.gz"), emit: reads | ||
| shell: | ||
| ''' | ||
| echo "Number of output reads: !{n_reads}" | ||
| n_lines=$(expr !{n_reads} \\* 4) | ||
| echo "Number of output lines: ${n_lines}" | ||
| if [ $(echo "!{reads}" | wc -w) -eq 2 ]; then | ||
| echo "Processing paired-end reads" | ||
| o1=!{sample}_trunc_1.fastq.gz | ||
| o2=!{sample}_trunc_2.fastq.gz | ||
| zcat !{reads[0]} | head -n ${n_lines} | gzip -c > ${o1} | ||
| zcat !{reads[1]} | head -n ${n_lines} | gzip -c > ${o2} | ||
| else | ||
| echo "Processing single-end reads" | ||
| o=!{sample}_trunc.fastq.gz | ||
| zcat !{reads[0]} | head -n ${n_lines} | gzip -c > ${o} | ||
| fi | ||
| o1=!{sample}_trunc_1.fastq.gz | ||
| o2=!{sample}_trunc_2.fastq.gz | ||
| zcat !{reads[0]} | head -n ${n_lines} | gzip -c > ${o1} | ||
| zcat !{reads[1]} | head -n ${n_lines} | gzip -c > ${o2} | ||
| ''' | ||
| } | ||
|
|
||
| process TRUNCATE_CONCAT_SINGLE { | ||
| label "single" | ||
| label "BBTools" | ||
| input: | ||
| tuple val(sample), path(reads) | ||
| val n_reads | ||
| output: | ||
| tuple val(sample), path("${sample}_trunc.fastq.gz"), emit: reads | ||
| shell: | ||
| ''' | ||
| echo "Number of output reads: !{n_reads}" | ||
| n_lines=$(expr !{n_reads} \\* 4) | ||
| echo "Number of output lines: ${n_lines}" | ||
| o=!{sample}_trunc.fastq.gz | ||
| zcat !{reads[0]} | head -n ${n_lines} | gzip -c > ${o} | ||
| ''' | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,45 @@ | ||
| /*********** | ||
| | WORKFLOW | | ||
| ***********/ | ||
|
|
||
| workflow LOAD_SAMPLESHET { | ||
| take: | ||
| sample_sheet | ||
| main: | ||
| if (params.single_end) { | ||
| if (params.grouping) { | ||
| samplesheet = Channel | ||
| .fromPath(params.sample_sheet) | ||
| .splitCsv(header: true) | ||
| .map { row -> tuple(row.sample, file(row.fastq), row.group) } | ||
| samplesheet_ch = samplesheet.map { sample, read, group -> tuple(sample, [read]) } | ||
| group_ch = samplesheet.map { sample, read, group -> tuple(sample, group) } | ||
| } else { | ||
| samplesheet = Channel | ||
| .fromPath(params.sample_sheet) | ||
| .splitCsv(header: true) | ||
| .map { row -> tuple(row.sample, file(row.fastq)) } | ||
| samplesheet_ch = samplesheet.map { sample, read -> tuple(sample, [read]) } | ||
| group_ch = Channel.empty() | ||
| } | ||
| } else { | ||
| if (params.grouping) { | ||
| samplesheet = Channel | ||
| .fromPath(params.sample_sheet) | ||
| .splitCsv(header: true) | ||
| .map { row -> tuple(row.sample, file(row.fastq_1), file(row.fastq_2), row.group) } | ||
| samplesheet_ch = samplesheet.map { sample, read1, read2, group -> tuple(sample, [read1, read2]) } | ||
| group_ch = samplesheet.map { sample, read1, read2, group -> tuple(sample, group) } | ||
| } else { | ||
| samplesheet = Channel | ||
| .fromPath(params.sample_sheet) | ||
| .splitCsv(header: true) | ||
| .map { row -> tuple(row.sample, file(row.fastq_1), file(row.fastq_2)) } | ||
| samplesheet_ch = samplesheet.map { sample, read1, read2 -> tuple(sample, [read1, read2]) } | ||
| group_ch = Channel.empty() | ||
| } | ||
| } | ||
| emit: | ||
| samplesheet = samplesheet_ch | ||
| group = group_ch | ||
| } |
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