diff --git a/donut_falls.nf b/donut_falls.nf index 6b442b2..daaadab 100755 --- a/donut_falls.nf +++ b/donut_falls.nf @@ -1186,8 +1186,8 @@ process nanoplot { output: path "nanoplot/*", emit: everything - path "nanoplot/*_NanoStats.txt", emit: stats - path "nanoplot/*_NanoStats.csv", emit: summary + path "nanoplot/${meta.id}_NanoStats.txt", emit: stats + path "nanoplot/${meta.id}_NanoStats.csv", emit: summary path "versions.yml", emit: versions when: @@ -1396,7 +1396,7 @@ process raven { } process summary { - tag "${meta.id}" + tag "Creating summary" label "process_single" publishDir "${params.outdir}/summary", mode: 'copy' container 'staphb/multiqc:1.19' @@ -1412,9 +1412,6 @@ process summary { when: task.ext.when == null || task.ext.when - shell: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" """ #!/usr/bin/env python3 @@ -1736,7 +1733,6 @@ process test_donut_falls { output: tuple val("df"), file("test_files/test.fastq.gz"), file("test_files/test_{1,2}.fastq.gz"), emit: fastq - tuple val("dflr"), file("test_files/test.fastq.gz"), emit: lrfastq when: task.ext.when == null || task.ext.when @@ -1748,6 +1744,29 @@ process test_donut_falls { """ } +process test_donut_falls_lr { + tag "Downloading R10.4 reads" + label "process_single" + publishDir "${params.outdir}/test_files/df", mode: 'copy' + container 'staphb/multiqc:1.19' + //errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'} + time '1h' + + output: + tuple val("dflr"), file("test_files/test_lr.fastq.gz"), emit: fastq + + when: + task.ext.when == null || task.ext.when + + shell: + """ + wget --quiet https://zenodo.org/records/10733190/files/df_test_files.tar.gz?download=1 -O dataset.tar.gz + tar -xvf dataset.tar.gz + + mv test_files/test.fastq.gz test_files/test_lr.fastq.gz + """ +} + // ##### ##### ##### ##### ##### ##### ##### ##### ##### ##### // Donut Falls @@ -1972,9 +1991,9 @@ workflow DONUT_FALLS { versions(ch_collated_versions) ch_summary = ch_summary.mix(versions.out.versions) - summary(ch_summary.collect()) + summary(ch_summary.unique().collect()) - multiqc(ch_summary.collect()) + multiqc(ch_summary.unique().collect()) ch_consensus .combine(circulocov_summary) @@ -2010,6 +2029,8 @@ workflow { test_donut_falls() + test_donut_falls_lr() + test_donut_falls.out.fastq .map { it -> meta = [id:it[0]] @@ -2019,7 +2040,7 @@ workflow { } .set{ ch_test_df_out } - test_donut_falls.out.lrfastq + test_donut_falls_lr.out.fastq .map { it -> meta = [id:it[0]] tuple( meta,