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Fix lack of fastqc in multiqc report #44

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Apr 10, 2024
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1 change: 1 addition & 0 deletions CHANGELOG.md
Original file line number Diff line number Diff line change
Expand Up @@ -20,6 +20,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#40](https://github.com/nf-core/riboseq/pull/40) - Ribotricer orf prediction ([@pinin4fjords](https://github.com/pinin4fjords), review by [@maxulysse](https://github.com/maxulysse))
- [#42](https://github.com/nf-core/riboseq/pull/42) - Add alignment based quantification with Salmon ([@pinin4fjords](https://github.com/pinin4fjords), review by [@maxulysse](https://github.com/maxulysse))
- [#43](https://github.com/nf-core/riboseq/pull/43) - Add translational efficiency analysis with anota2seq ([@pinin4fjords](https://github.com/pinin4fjords), review by )
- [#44](Fix lack of fastqc in multiqc report) - Fix lack of fastqc in multiqc report ([@pinin4fjords](https://github.com/pinin4fjords), review by [@maxulysse](https://github.com/maxulysse))

Initial release of nf-core/riboseq, created with the [nf-core](https://nf-co.re/) template.

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4 changes: 2 additions & 2 deletions assets/multiqc_config.yml
Original file line number Diff line number Diff line change
Expand Up @@ -49,14 +49,14 @@ module_order:
name: "FastQC (raw)"
info: "This section of the report shows FastQC results before adapter trimming."
path_filters:
- "./fastqc/raw/*.zip"
- "*_raw_fastqc.zip"
- cutadapt
- fastp
- fastqc:
name: "FastQC (trimmed)"
info: "This section of the report shows FastQC results after adapter trimming."
path_filters:
- "./fastqc/trim/*.zip"
- "*_trimmed_fastqc.zip"

# Don't show % Dups in the General Stats table (we have this from Picard)
table_columns_visible:
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3 changes: 3 additions & 0 deletions conf/modules.config
Original file line number Diff line number Diff line change
Expand Up @@ -193,6 +193,7 @@ if (!(params.skip_fastqc || params.skip_qc)) {
if (params.trimmer == 'trimgalore') {
process {
withName: '.*:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC' {
ext.prefix = { "${meta.id}_raw" }
ext.args = '--quiet'
publishDir = [
path: { "${params.outdir}/preprocessing/fastqc" },
Expand All @@ -206,6 +207,7 @@ if (!(params.skip_fastqc || params.skip_qc)) {
if (params.trimmer == 'fastp') {
process {
withName: '.*:FASTQ_FASTQC_UMITOOLS_FASTP:FASTQC_RAW' {
ext.prefix = { "${meta.id}_raw" }
ext.args = '--quiet'
publishDir = [
path: { "${params.outdir}/preprocessing/fastqc" },
Expand All @@ -215,6 +217,7 @@ if (!(params.skip_fastqc || params.skip_qc)) {
}

withName: '.*:FASTQ_FASTQC_UMITOOLS_FASTP:FASTQC_TRIM' {
ext.prefix = { "${meta.id}_trimmed" }
ext.args = '--quiet'
publishDir = [
path: { "${params.outdir}/${params.trimmer}/fastqc" },
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