DSL2 - Genotyping Input Updates

assets/schema_fasta.json

@@ -124,6 +124,7 @@
             "genotyping_reference_ploidy": {
                 "type": "integer",
                 "meta": ["genotyping_ploidy"],
+                "default": 2,
                 "errorMessage": "Organism ploidy for GATK or FreeBayes must be provided as integers."
             },
             "genotyping_gatk_dbsnp": {

docs/development/manual_tests.md

@@ -991,7 +991,7 @@ nextflow run main.nf -profile test,docker --outdir ./results -w work/ -resume --
 ## Gatk UG on trimmed reads. Skip bcftools stats.
 ## Expect: One VCF + .tbi index per sample/reference combination, based on the trimmed bams (this actually shows on the IndelRealigner step and not the UG step).  No IR directory. No bcftools_stats file per VCF.
 ## Checked that the input bam for the UG jobs indeed had trimmed reads. (The full UDG sample has untrimmed bams.)
-nextflow run main.nf -profile test,docker --outdir ./results -w work/ -resume --run_genotyping --genotyping_tool 'ug' --genotyping_source 'trimmed' -ansi-log false -dump-channels --skip_bcftools_stats \
+nextflow run main.nf -profile test,docker --outdir ./results -w work/ -resume --run_genotyping --genotyping_tool 'ug' --genotyping_source 'trimmed' -ansi-log false -dump-channels --genotyping_skip_bcftools_stats \
   --run_trim_bam \
   --damage_manipulation_bamutils_trim_double_stranded_none_udg_left 5 \
   --damage_manipulation_bamutils_trim_double_stranded_none_udg_right 7 \
@@ -1030,7 +1030,7 @@ nextflow run main.nf -profile test,docker --outdir ./results -w work/ -resume --
 ```bash
 ## Attempt to run Gatk HC on trimmed reads, without activating trimming.
 ## Expect: FAILURE. Cannot set genotyping source to ;trimmed' without trimming.
-nextflow run main.nf -profile test,docker --outdir ./results -w work/ -resume --run_genotyping --genotyping_tool 'hc' --genotyping_source 'trimmed' -ansi-log false -dump-channels --skip_bcftools_stats \
+nextflow run main.nf -profile test,docker --outdir ./results -w work/ -resume --run_genotyping --genotyping_tool 'hc' --genotyping_source 'trimmed' -ansi-log false -dump-channels --genotyping_skip_bcftools_stats \
   --genotyping_gatk_hc_emitrefconf 'BP_RESOLUTION' \
   --genotyping_gatk_hc_out_mode 'EMIT_ALL_ACTIVE_SITES'
 ```
@@ -1039,7 +1039,7 @@ nextflow run main.nf -profile test,docker --outdir ./results -w work/ -resume --
 ## Gatk HC on trimmed reads, with different out mode and emit confidence. Skip bcftools stats.
 ## Expect: One VCF + .tbi index per sample/reference combination.
 ## Checked .command.sh for correct args.
-nextflow run main.nf -profile test,docker --outdir ./results -w work/ -resume --run_genotyping --genotyping_tool 'hc' --genotyping_source 'trimmed' --run_trim_bam -ansi-log false -dump-channels --skip_bcftools_stats \
+nextflow run main.nf -profile test,docker --outdir ./results -w work/ -resume --run_genotyping --genotyping_tool 'hc' --genotyping_source 'trimmed' --run_trim_bam -ansi-log false -dump-channels --genotyping_skip_bcftools_stats \
   --genotyping_gatk_hc_emitrefconf 'BP_RESOLUTION' \
   --genotyping_gatk_hc_out_mode 'EMIT_ALL_ACTIVE_SITES'
 ```
@@ -1063,7 +1063,7 @@ nextflow run main.nf -profile test,docker --outdir ./results -w work/ -resume --
 ## Freebayes on trimmed reads. Different options, and skip bcftools stats.
 ## Expect: One VCF + .tbi index per sample/reference combination.
 ## Checked .command.sh for correct args.
-nextflow run main.nf -profile test,docker --outdir ./results -w work/ -resume --run_genotyping --genotyping_tool 'freebayes' --genotyping_source 'trimmed' -ansi-log false -dump-channels --skip_bcftools_stats \
+nextflow run main.nf -profile test,docker --outdir ./results -w work/ -resume --run_genotyping --genotyping_tool 'freebayes' --genotyping_source 'trimmed' -ansi-log false -dump-channels --genotyping_skip_bcftools_stats \
   --run_trim_bam \
   --genotyping_freebayes_skip_coverage 10 \
   --genotyping_freebayes_min_alternate_count 2 \

docs/usage.md

@@ -102,7 +102,7 @@ Only the `reference_name`, and `fasta` columns are mandatory, whereas all other
 | pmdtools_bed_for_masking    | No       | Optional path to SNP capture BED file to mask the reference for PMDtools                                                   |
 | sexdeterrmine_snp_bed       | No       | Optional path to SNP capture bed files for genetic sex estimation with SexDetERRmine                                       |
 | bedtools_feature_file       | No       | Optional path to feature file for coverage calculation with bedtools                                                       |
-| genotyping_reference_ploidy | No       | Optional integer to specify organism ploidy for genotyping with GATK or FreeBayes                                          |
+| genotyping_reference_ploidy | No       | Optional integer to specify organism ploidy for genotyping with GATK or FreeBayes (by default set to 2)                    |
 | genotyping_gatk_dbsnp       | No       | Optional path to SNP annotation file for genotyping with GATK                                                              |
 
 Files for `fai`, `dict`, `mapper_index` will be generated by the pipeline for you if not specified.

modules.json

@@ -235,6 +235,11 @@
                         "git_sha": "f0719ae309075ae4a291533883847c3f7c441dad",
                         "installed_by": ["modules"]
                     },
+                    "picard/addorreplacereadgroups": {
+                        "branch": "master",
+                        "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
+                        "installed_by": ["modules"]
+                    },
                     "picard/createsequencedictionary": {
                         "branch": "master",
                         "git_sha": "20b0918591d4ba20047d7e13e5094bcceba81447",