Merge pull request #748 from nf-core/validation-fixes-patch

Fix bedtools annotation file condition and re-add defaults

Author: jfy133

CHANGELOG.md

@@ -16,6 +16,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 - Updated template to nf-core/tools 1.14
 - [#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
 - [#751](https://github.com/nf-core/eager/pull/751) - Added missing label to mtnucratio
+- General code cleanup and standarisation of parameters with no default setting
 
 ### `Dependencies`
 

main.nf

@@ -46,7 +46,7 @@ if ( params.skip_collapse && params.skip_trim ) {
 }
 
 // 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."
 }
 

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`"