all tests work

sanger-tol · Sep 17, 2023 · 1023126 · 1023126
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diff --git a/assets/test/mMelMel3.1.buscogenes.dmnd b/assets/test/mMelMel3.1.buscogenes.dmnd
@@ -0,0 +1 @@
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diff --git a/assets/test/samplesheet_raw.csv b/assets/test/samplesheet_raw.csv
@@ -0,0 +1,4 @@
+sample,datatype,datafile
+mMelMel1,illumina,/lustre/scratch123/tol/resources/nextflow/test-data/Meles_meles/genomic_data/mMelMel1/illumina/31231_3#1_subset.cram
+mMelMel2,illumina,/lustre/scratch123/tol/resources/nextflow/test-data/Meles_meles/genomic_data/mMelMel2/illumina/31231_4#1_subset.cram
+mMelMel3,hic,/lustre/scratch123/tol/resources/nextflow/test-data/Meles_meles/genomic_data/mMelMel3/hic-arima2/35528_2#1_subset.cram
diff --git a/conf/test_raw.config b/conf/test_raw.config
@@ -0,0 +1,36 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Nextflow config file for running minimal tests
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Defines input files and everything required to run a fast and simple pipeline test.
+
+    Use as follows:
+        nextflow run sanger-tol/blobtoolkit -profile test_raw,<docker/singularity> --outdir <OUTDIR>
+
+----------------------------------------------------------------------------------------
+*/
+
+params {
+    config_profile_name        = 'Test profile'
+    config_profile_description = 'Minimal test dataset to check pipeline function'
+
+    // Limit resources so that this can run on GitHub Actions
+    max_cpus   = 2
+    max_memory = '6.GB'
+    max_time   = '6.h'
+
+    // Input test data
+    // Specify the paths to your test data
+    // Give any required params for the test so that command line flags are not needed
+    input     = "${projectDir}/assets/test/samplesheet_raw.csv"
+
+    // Fasta references
+    fasta     = "/lustre/scratch123/tol/resources/nextflow/test-data/Meles_meles/assembly/release/mMelMel3.1_paternal_haplotype/GCA_922984935.2.subset.fasta.gz"
+    accession = "GCA_922984935.2"
+    taxon     = "Meles meles"
+
+    // Databases
+    taxdump   = "/lustre/scratch123/tol/teams/grit/geval_pipeline/btk_databases/taxdump"
+    busco     = "/lustre/scratch123/tol/resources/nextflow/busco_2021_06_reduced/"
+    uniprot   = "${projectDir}/assets/test/mCerEla1.1.buscogenes.dmnd"
+}
diff --git a/modules.json b/modules.json
@@ -8,94 +8,63 @@
                     "busco": {
                         "branch": "master",
                         "git_sha": "6d6552cb582f56b6101c452e16ee7c23073f91de",
-                        "installed_by": [
-                            "modules"
-                        ],
+                        "installed_by": ["modules"],
                         "patch": "modules/nf-core/busco/busco.diff"
                     },
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
                         "git_sha": "05c280924b6c768d484c7c443dad5e605c4ff4b4",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "diamond/blastp": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "fastawindows": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "goat/taxonsearch": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "gunzip": {
                         "branch": "master",
                         "git_sha": "e06548bfa36ee31869b81041879dd6b3a83b1d57",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "minimap2/align": {
                         "branch": "master",
                         "git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "mosdepth": {
                         "branch": "master",
                         "git_sha": "ebb27711cd5f4de921244bfa81c676504072d31c",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "multiqc": {
                         "branch": "master",
                         "git_sha": "a6e11ac655e744f7ebc724be669dd568ffdc0e80",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "samtools/fasta": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "samtools/index": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": [
-                            "modules"
-                        ]
-                    },
-                    "samtools/sort": {
-                        "branch": "master",
-                        "git_sha": "a0f7be95788366c1923171e358da7d049eb440f9",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "samtools/view": {
                         "branch": "master",
                         "git_sha": "3ffae3598260a99e8db3207dead9f73f87f90d1f",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     }
                 }
             },
@@ -104,4 +73,4 @@
             }
         }
     }
-}
+}
diff --git a/modules/nf-core/busco/main.nf b/modules/nf-core/busco/main.nf
diff --git a/modules/nf-core/samtools/sort/main.nf b/modules/nf-core/samtools/sort/main.nf
diff --git a/modules/nf-core/samtools/sort/meta.yml b/modules/nf-core/samtools/sort/meta.yml
diff --git a/nextflow.config b/nextflow.config
@@ -13,6 +13,7 @@ params {
     // Input options
     input                      = null
     yaml                       = null
+    align                      = false
 
     // Reference options    
     fasta                      = null
@@ -177,6 +178,7 @@ profiles {
     }
     cleanup   { cleanup = true                        }
     test      { includeConfig 'conf/test.config'      }
+    test_raw  { includeConfig 'conf/test_raw.config   }
     test_full { includeConfig 'conf/test_full.config' }
 }
 

diff --git a/subworkflows/local/coverage_stats.nf b/subworkflows/local/coverage_stats.nf
@@ -29,11 +29,7 @@ workflow COVERAGE_STATS {
         | map { meta, cram -> [ meta, cram, [] ] }
         | set { ch_cram_crai}
 
-        fasta
-        | map { meta, fasta -> fasta }
-        | set { ch_fasta }
-
-        SAMTOOLS_VIEW ( ch_cram_crai, ch_fasta, [] )
+        SAMTOOLS_VIEW ( ch_cram_crai, fasta, [] )
         ch_versions = ch_versions.mix ( SAMTOOLS_VIEW.out.versions.first() )
 
         SAMTOOLS_VIEW.out.bam

diff --git a/subworkflows/local/minimap_alignment.nf b/subworkflows/local/minimap_alignment.nf
@@ -2,14 +2,13 @@
 // Optional alignment subworkflow using Minimap2
 //
 
-include { SAMTOOLS_FASTA                  } from '../../../modules/nf-core/samtools/fasta/main'
-include { MINIMAP2_ALIGN as MINIMAP2_HIC  } from '../../../modules/nf-core/minimap2/align/main'
-include { MINIMAP2_ALIGN as MINIMAP2_ILMN } from '../../../modules/nf-core/minimap2/align/main'
-include { MINIMAP2_ALIGN as MINIMAP2_CCS  } from '../../../modules/nf-core/minimap2/align/main'
-include { MINIMAP2_ALIGN as MINIMAP2_CLR  } from '../../../modules/nf-core/minimap2/align/main'
-include { MINIMAP2_ALIGN as MINIMAP2_ONT  } from '../../../modules/nf-core/minimap2/align/main'
-include { SAMTOOLS_SORT                   } from '../../../modules/nf-core/samtools/sort/main'
-include { SAMTOOLS_INDEX                  } from '../../../modules/nf-core/samtools/index/main'
+include { SAMTOOLS_FASTA                  } from '../../modules/nf-core/samtools/fasta/main'
+include { MINIMAP2_ALIGN as MINIMAP2_HIC  } from '../../modules/nf-core/minimap2/align/main'
+include { MINIMAP2_ALIGN as MINIMAP2_ILMN } from '../../modules/nf-core/minimap2/align/main'
+include { MINIMAP2_ALIGN as MINIMAP2_CCS  } from '../../modules/nf-core/minimap2/align/main'
+include { MINIMAP2_ALIGN as MINIMAP2_CLR  } from '../../modules/nf-core/minimap2/align/main'
+include { MINIMAP2_ALIGN as MINIMAP2_ONT  } from '../../modules/nf-core/minimap2/align/main'
+include { SAMTOOLS_INDEX                  } from '../../modules/nf-core/samtools/index/main'
 
 
 workflow MINIMAP2_ALIGNMENT {
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