From e971cacb14b021a695b1203f5774f73a4b888905 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Mon, 25 Feb 2019 21:11:56 +0100 Subject: [PATCH 1/6] Made polyG param clearer what it is --- main.nf | 22 +++++++++++----------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/main.nf b/main.nf index 7513f0649..8d7c9050f 100644 --- a/main.nf +++ b/main.nf @@ -50,7 +50,7 @@ def helpMessage() { --skip_deduplication Complexity Filtering - --complexity_filtering Run poly-G removal on FASTQ files + --complexity_filter_poly_g Run poly-G removal on FASTQ files --complexity_filter_poly_g_min Specify length of poly-g min for clipping to be performed (default: 10) Clipping / Merging @@ -151,7 +151,7 @@ params.skip_qualimap = false params.skip_deduplication = false //Complexity filtering reads -params.complexity_filter = false +params.complexity_filter_poly_g = false params.complexity_filter_poly_g_min = 10 //Read clipping and merging parameters @@ -291,14 +291,14 @@ if( params.readPaths ){ .from( params.readPaths ) .map { row -> [ row[0], [ file( row[1][0] ) ] ] } .ifEmpty { exit 1, "params.readPaths or params.bams was empty - no input files supplied!" } - .into { ch_read_files_clip; ch_read_files_fastqc; ch_read_files_complexity_filtering } + .into { ch_read_files_clip; ch_read_files_fastqc; ch_read_files_complexity_filter_poly_g } ch_bam_to_fastq_convert = Channel.empty() } else if (!params.bam){ Channel .from( params.readPaths ) .map { row -> [ row[0], [ file( row[1][0] ), file( row[1][1] ) ] ] } .ifEmpty { exit 1, "params.readPaths or params.bams was empty - no input files supplied!" } - .into { ch_read_files_clip; ch_read_files_fastqc; ch_read_files_complexity_filtering } + .into { ch_read_files_clip; ch_read_files_fastqc; ch_read_files_complexity_filter_poly_g } ch_bam_to_fastq_convert = Channel.empty() } else { Channel @@ -310,7 +310,7 @@ if( params.readPaths ){ //Set up clean channels ch_read_files_fastqc = Channel.empty() - ch_read_files_complexity_filtering = Channel.empty() + ch_read_files_complexity_filter_poly_g = Channel.empty() ch_read_files_clip = Channel.empty() } } else if (!params.bam){ @@ -318,7 +318,7 @@ if( params.readPaths ){ .fromFilePairs( params.reads, size: params.singleEnd ? 1 : 2 ) .ifEmpty { exit 1, "Cannot find any reads matching: ${params.reads}\nNB: Path needs" + "to be enclosed in quotes!\nNB: Path requires at least one * wildcard!\nIf this is single-end data, please specify --singleEnd on the command line." } - .into { ch_read_files_clip; ch_read_files_fastqc; ch_read_files_complexity_filtering } + .into { ch_read_files_clip; ch_read_files_fastqc; ch_read_files_complexity_filter_poly_g } ch_bam_to_fastq_convert = Channel.empty() } else { Channel @@ -331,7 +331,7 @@ if( params.readPaths ){ //Set up clean channels ch_read_files_fastqc = Channel.empty() - ch_read_files_complexity_filtering = Channel.empty() + ch_read_files_complexity_filter_poly_g = Channel.empty() ch_read_files_clip = Channel.empty() } @@ -548,13 +548,13 @@ process fastp { tag "$name" publishDir "${params.outdir}/FastP", mode: 'copy' - when: params.complexity_filter + when: params.complexity_filter_poly_g input: - set val(name), file(reads) from ch_read_files_complexity_filtering.mix(ch_read_files_converted_fastp) + set val(name), file(reads) from ch_read_files_complexity_filter_poly_g.mix(ch_read_files_converted_fastp) output: - set val(name), file("*pG.fq.gz") into ch_clipped_reads_complexity_filtered + set val(name), file("*pG.fq.gz") into ch_clipped_reads_complexity_filtered_poly_g file("*.json") into ch_fastp_for_multiqc script: @@ -582,7 +582,7 @@ process adapter_removal { when: !params.bam input: - set val(name), file(reads) from ( params.complexity_filter ? ch_clipped_reads_complexity_filtered : ch_read_files_clip ) + set val(name), file(reads) from ( params.complexity_filter_poly_g ? ch_clipped_reads_complexity_filtered_poly_g : ch_read_files_clip ) output: file "*.combined*.gz" into (ch_clipped_reads, ch_clipped_reads_for_fastqc,ch_clipped_reads_circularmapper,ch_clipped_reads_bwamem) From 0feeb191517554876034bbfcd47ee42c8b8505fd Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Mon, 25 Feb 2019 21:31:54 +0100 Subject: [PATCH 2/6] Update CHANGELOG.md --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 315efb773..c01691fce 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,7 +10,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. ### `Fixed` * [#145](https://github.com/nf-core/eager/issues/145) - Added Picard Memory Handling [fix](https://github.com/nf-core/eager/issues/144) - +* Clarified `--complexity_filter` flag to be specifically for poly G trimming. ## [2.0.5] - 2019-01-28 From 29306df77f93746c15bebaed2a734441e6115c3e Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Mon, 25 Feb 2019 21:33:15 +0100 Subject: [PATCH 3/6] Updated ploy G trim flag --- docs/usage.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/usage.md b/docs/usage.md index dbb3889a1..d2caf6821 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -299,7 +299,7 @@ Turns off duplicate removal methods DeDup and MarkDuplicates respectively. No du ## Complexity Filtering Options -### `--complexity_filter` +### `--complexity_filter_poly_g` Performs a poly-G tail removal step in the beginning of the pipeline, if turned on. This can be useful for trimming ploy-G tails from short-fragments sequenced on two-colour Illumina chemistry such as NextSeqs (where no-fluorescence is read as a G on two-colour chemistry), which can inflate reported GC content values. From bc02be25023f53d8a7c4cd8d8160bc172a72d3ea Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Mon, 25 Feb 2019 21:36:22 +0100 Subject: [PATCH 4/6] Update CHANGELOG.md --- CHANGELOG.md | 1 - 1 file changed, 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index c01691fce..a5bf6fe11 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,7 +10,6 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. ### `Fixed` * [#145](https://github.com/nf-core/eager/issues/145) - Added Picard Memory Handling [fix](https://github.com/nf-core/eager/issues/144) -* Clarified `--complexity_filter` flag to be specifically for poly G trimming. ## [2.0.5] - 2019-01-28 From 7836ab8df5f8d64638a87f7fb7a67d6a6e4b549a Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Mon, 25 Feb 2019 21:41:51 +0100 Subject: [PATCH 5/6] Update CHANGELOG.md --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index a5bf6fe11..9084fd20d 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,6 +10,8 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. ### `Fixed` * [#145](https://github.com/nf-core/eager/issues/145) - Added Picard Memory Handling [fix](https://github.com/nf-core/eager/issues/144) +* Clarified `--complexity_filter` flag to be specifically for poly G trimming. + ## [2.0.5] - 2019-01-28 From 6d13545b86d3636e8d6aae0465e7cf61adbd8dc1 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Mon, 25 Feb 2019 21:46:56 +0100 Subject: [PATCH 6/6] Added fastP position to MultiQC config --- conf/multiqc_config.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/conf/multiqc_config.yaml b/conf/multiqc_config.yaml index 8e561e902..1b6bdaa63 100644 --- a/conf/multiqc_config.yaml +++ b/conf/multiqc_config.yaml @@ -9,6 +9,7 @@ top_modules: - '*_fastqc.zip' path_filters_exclude: - '*.combined.prefixed_fastqc.zip' + - 'fastp' - 'adapterRemoval' - 'fastqc': name: 'FastQC (post-AdapterRemoval)'