From 07943c32a8f815c7d35ec3bdec6e6cb7ea75b18f Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Fri, 14 May 2021 15:00:11 +0200 Subject: [PATCH 1/4] Fix bedtools annotation file condition and re-add defaults --- main.nf | 4 ++-- nextflow_schema.json | 7 +++++++ 2 files changed, 9 insertions(+), 2 deletions(-) diff --git a/main.nf b/main.nf index df40a6787..6f5a1a8b8 100644 --- a/main.nf +++ b/main.nf @@ -40,13 +40,13 @@ if (!has_extension(params.input, "tsv") && params.skip_collapse && params.singl exit 1, "[nf-core/eager] error: --skip_collapse can only be set for paired_end samples." } -// Validate not trying to both skip collapse and skip trim +// Validate not trying to both skip collapse -profile test_tsv,docker --run_bedtools_coverage --anno_file 'https://github.com/nf-core/test-datasets/raw/eager/reference/Mammoth/Mammoth_MT_Krause.gff3'and skip trim if ( params.skip_collapse && params.skip_trim ) { exit 1, "[nf-core/eager error]: you have specified to skip both merging and trimming of paired end samples. Use --skip_adapterremoval instead." } // Bedtools validation -if(params.run_bedtools_coverage && params.anno_file ){ +if(params.run_bedtools_coverage && !params.anno_file ){ exit 1, "[nf-core/eager] error: you have turned on bedtools coverage, but not specified a BED or GFF file with --anno_file. Please validate your parameters." } diff --git a/nextflow_schema.json b/nextflow_schema.json index a33f5455c..64814061c 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -616,6 +616,7 @@ }, "bt2n": { "type": "integer", + "default": 0, "description": "Specify the -N parameter for bowtie2 (mismatches in seed). This will override defaults from alignmode/sensitivity.", "fa_icon": "fas fa-sort-numeric-down", "help_text": "The number of mismatches allowed in the seed during seed-and-extend procedure of Bowtie2. This will override any values set with `--bt2_sensitivity`. Can either be 0 or 1. Default: 0 (i.e. use`--bt2_sensitivity` defaults).\n\n> Modifies Bowtie2 parameters: `-N`", @@ -626,18 +627,21 @@ }, "bt2l": { "type": "integer", + "default": 0, "description": "Specify the -L parameter for bowtie2 (length of seed substrings). This will override defaults from alignmode/sensitivity.", "fa_icon": "fas fa-ruler-horizontal", "help_text": "The length of the seed sub-string to use during seeding. This will override any values set with `--bt2_sensitivity`. Default: 0 (i.e. use`--bt2_sensitivity` defaults: [20 for local and 22 for end-to-end](http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml#command-line).\n\n> Modifies Bowtie2 parameters: `-L`" }, "bt2_trim5": { "type": "integer", + "default": 0, "description": "Specify number of bases to trim off from 5' (left) end of read before alignment.", "fa_icon": "fas fa-cut", "help_text": "Number of bases to trim at the 5' (left) end of read prior alignment. Maybe useful when left-over sequencing artefacts of in-line barcodes present Default: 0\n\n> Modifies Bowtie2 parameters: `-bt2_trim5`" }, "bt2_trim3": { "type": "integer", + "default": 0, "description": "Specify number of bases to trim off from 3' (right) end of read before alignment.", "fa_icon": "fas fa-cut", "help_text": "Number of bases to trim at the 3' (right) end of read prior alignment. Maybe useful when left-over sequencing artefacts of in-line barcodes present Default: 0.\n\n> Modifies Bowtie2 parameters: `-bt2_trim3`" @@ -695,12 +699,14 @@ }, "bam_mapping_quality_threshold": { "type": "integer", + "default": 0, "description": "Minimum mapping quality for reads filter.", "fa_icon": "fas fa-greater-than-equal", "help_text": "Specify a mapping quality threshold for mapped reads to be kept for downstream analysis. By default keeps all reads and is therefore set to `0` (basically doesn't filter anything).\n\n> Modifies samtools view parameter: `-q`" }, "bam_filter_minreadlength": { "type": "integer", + "default": 0, "fa_icon": "fas fa-ruler-horizontal", "description": "Specify minimum read length to be kept after mapping.", "help_text": "Specify minimum length of mapped reads. This filtering will apply at the same time as mapping quality filtering.\n\nIf used _instead_ of minimum length read filtering at AdapterRemoval, this can be useful to get more realistic endogenous DNA percentages, when most of your reads are very short (e.g. in single-stranded libraries) and would otherwise be discarded by AdapterRemoval (thus making an artificially small denominator for a typical endogenous DNA calculation). Note in this context you should not perform mapping quality filtering nor discarding of unmapped reads to ensure a correct denominator of all reads, for the endogenous DNA calculation.\n\n> Modifies filter_bam_fragment_length.py parameter: `-l`" @@ -1065,6 +1071,7 @@ }, "freebayes_g": { "type": "integer", + "default": 0, "description": "Specify to skip over regions of high depth by discarding alignments overlapping positions where total read depth is greater than specified in --freebayes_C.", "fa_icon": "fab fa-think-peaks", "help_text": "Specify to skip over regions of high depth by discarding alignments overlapping positions where total read depth is greater than specified C. Not set by default.\n\n> Modifies freebayes parameter: `-g`" From d8ca43f42a1f45b8d010a3aae6d749a3692161ee Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Mon, 17 May 2021 10:05:10 +0200 Subject: [PATCH 2/4] Update main.nf --- main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/main.nf b/main.nf index 6f5a1a8b8..3c42e9593 100644 --- a/main.nf +++ b/main.nf @@ -40,7 +40,7 @@ if (!has_extension(params.input, "tsv") && params.skip_collapse && params.singl exit 1, "[nf-core/eager] error: --skip_collapse can only be set for paired_end samples." } -// Validate not trying to both skip collapse -profile test_tsv,docker --run_bedtools_coverage --anno_file 'https://github.com/nf-core/test-datasets/raw/eager/reference/Mammoth/Mammoth_MT_Krause.gff3'and skip trim +// Validate not trying to both skip collapse and skip trim if ( params.skip_collapse && params.skip_trim ) { exit 1, "[nf-core/eager error]: you have specified to skip both merging and trimming of paired end samples. Use --skip_adapterremoval instead." } From 63b52e51c3c7c28673e79a6407eebc0313b27e3f Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Wed, 19 May 2021 09:45:24 +0200 Subject: [PATCH 3/4] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index b92fbed60..8c1d42f56 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -14,6 +14,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. - [#723](https://github.com/nf-core/eager/issues/723) - Fixes empty fields in TSV resulting in uninformative error - Updated template to nf-core/tools 1.14 +- General code cleanup and standarisation of parameters with no default setting ### `Dependencies` From 9883b85c92bf215fe50ba7ba66d9873480061113 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Wed, 19 May 2021 09:46:35 +0200 Subject: [PATCH 4/4] Update CHANGELOG.md --- CHANGELOG.md | 1 - 1 file changed, 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 48ad06b1a..093a84623 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -17,7 +17,6 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. - [#688](https://github.com/nf-core/eager/issues/688) - Clarified the pipeline is not just for humans and microbes, but also plants and animals, and also for modern DNA - General code cleanup and standarisation of parameters with no default setting - ### `Dependencies` ### `Deprecated`