diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index c35adfa..bb0d3cc 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -268,12 +268,8 @@ table_columns_visible: non-primary_alignments: False reads_MQ0_percent: False error_rate: False - Kraken: - "% Unclassified": False - "% Top 5": False - Bracken: - "% Unclassified": False - "% Top 5": False + Kraken: False + Bracken: False Centrifuge: False DIAMOND: queries_aligned: False diff --git a/conf/modules.config b/conf/modules.config index 8f1291a..2891590 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -158,7 +158,7 @@ process { [ path: { "${params.outdir}/porechop" }, mode: params.publish_dir_mode, - pattern: '*.fastq.gz', + pattern: '*_porechopped.fastq.gz', enabled: params.save_preprocessed_reads ], [ diff --git a/modules.json b/modules.json index 3d54d9d..2375da6 100644 --- a/modules.json +++ b/modules.json @@ -179,7 +179,8 @@ "porechop/porechop": { "branch": "master", "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", - "installed_by": ["modules"] + "installed_by": ["modules"], + "patch": "modules/nf-core/porechop/porechop/porechop-porechop.diff" }, "prinseqplusplus": { "branch": "master", diff --git a/modules/nf-core/porechop/porechop/main.nf b/modules/nf-core/porechop/porechop/main.nf index 5267910..37735ea 100644 --- a/modules/nf-core/porechop/porechop/main.nf +++ b/modules/nf-core/porechop/porechop/main.nf @@ -22,12 +22,16 @@ process PORECHOP_PORECHOP { def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" """ + ## To ensure ID matches rest of pipeline based on meta.id rather than input file name + mv $reads ${prefix}.fastq.gz + porechop \\ -i $reads \\ -t $task.cpus \\ $args \\ - -o ${prefix}.fastq.gz \\ + -o ${prefix}_porechopped.fastq.gz \\ > ${prefix}.log + cat <<-END_VERSIONS > versions.yml "${task.process}": porechop: \$( porechop --version ) diff --git a/modules/nf-core/porechop/porechop/porechop-porechop.diff b/modules/nf-core/porechop/porechop/porechop-porechop.diff new file mode 100644 index 0000000..897e1d2 --- /dev/null +++ b/modules/nf-core/porechop/porechop/porechop-porechop.diff @@ -0,0 +1,23 @@ +Changes in module 'nf-core/porechop/porechop' +--- modules/nf-core/porechop/porechop/main.nf ++++ modules/nf-core/porechop/porechop/main.nf +@@ -22,12 +22,16 @@ + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ ++ ## To ensure ID matches rest of pipeline based on meta.id rather than input file name ++ mv $reads ${prefix}.fastq.gz ++ + porechop \\ + -i $reads \\ + -t $task.cpus \\ + $args \\ +- -o ${prefix}.fastq.gz \\ ++ -o ${prefix}_porechopped.fastq.gz \\ + > ${prefix}.log ++ + cat <<-END_VERSIONS > versions.yml + "${task.process}": + porechop: \$( porechop --version ) + +************************************************************