From da0c068d1107513f5a6b1e24d4d645e4e577382c Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Sat, 16 Jul 2022 16:55:34 +0200 Subject: [PATCH 1/2] Fix missing defaults --- nextflow_schema.json | 23 +++++++++++++---------- 1 file changed, 13 insertions(+), 10 deletions(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index 2f0cd23c3..ca9f4fe6c 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -653,28 +653,28 @@ "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`", - "enum": [ - 0, - 1 - ] + "default": 0 }, "bt2l": { "type": "integer", "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`" + "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`", + "default": 0 }, "bt2_trim5": { "type": "integer", "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`" + "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`", + "default": 0 }, "bt2_trim3": { "type": "integer", "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`" + "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`", + "default": 0 }, "bt2_maxins": { "type": "integer", @@ -731,13 +731,15 @@ "type": "integer", "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`" + "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`", + "default": 0 }, "bam_filter_minreadlength": { "type": "integer", "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`" + "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`", + "default": 0 }, "bam_unmapped_type": { "type": "string", @@ -1168,7 +1170,8 @@ "type": "integer", "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`" + "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`", + "default": 0 }, "freebayes_p": { "type": "integer", From e325b38342a72f27e3b7e0df3d02b963d3a27134 Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Sat, 16 Jul 2022 16:56:35 +0200 Subject: [PATCH 2/2] Update changelgo --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index e9836d64b..dceb37c15 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,7 +7,6 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. ### `Added` - ### `Fixed` - [#882](https://github.com/nf-core/eager/pull/882) Define DSL1 execution explicitly, as new versions Nextflow made DSL2 default (♥ to & fix from @Lehmann-Fabian) @@ -18,6 +17,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. - [#895](https://github.com/nf-core/eager/issues/895) Output documentation typo fix and added location of output docs in pipeline summary (♥ to @RodrigoBarquera for reporting) - [#897](https://github.com/nf-core/eager/issues/897) Fix pipeline crash if no Kraken2 results generated (♥ to @alexandregilardet for reporting) - [#899](https://github.com/nf-core/eager/issues/897) Fix pipeline crash for circulargenerator if reference file does not end in .fasta (♥ to @scarlhoff for reporting) +- Fixed some missing default values in the nextflow parameter schema JSON ### `Dependencies`