Optional alignment subworkflow

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

bin/check_samplesheet.py

@@ -24,7 +24,10 @@ class RowChecker:
 
     """
 
-    VALID_FORMATS = (".cram",)
+    VALID_FORMATS = (
+        ".cram",
+        ".bam",
+    )
 
     VALID_DATATYPES = (
         "hic",

conf/modules.config

@@ -20,6 +20,30 @@ process {
         ]
     }
 
+    withName: "MINIMAP2_HIC" {
+        ext.args = "-ax sr"
+    }
+
+    withName: "MINIMAP2_ILMN" {
+        ext.args = "-ax sr"
+    }
+
+    withName: "MINIMAP2_CCS" {
+        ext.args = "-ax map-hifi --cs=short"
+    }
+
+    withName: "MINIMAP2_CLR" {
+        ext.args = "-ax map-pb"
+    }
+
+    withName: "MINIMAP2_ONT" {
+        ext.args = "-ax map-ont"
+    }
+
+    withName: "SAMTOOLS_INDEX" {
+        ext.args = "-c"
+    }
+
     withName: "GOAT_TAXONSEARCH" {
         ext.args = "-l -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"
+}

modules.json

@@ -7,13 +7,13 @@
                 "nf-core": {
                     "busco": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "6d6552cb582f56b6101c452e16ee7c23073f91de",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/busco/busco.diff"
                     },
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "05c280924b6c768d484c7c443dad5e605c4ff4b4",
                         "installed_by": ["modules"]
                     },
                     "diamond/blastp": {
@@ -33,23 +33,38 @@
                     },
                     "gunzip": {
                         "branch": "master",
-                        "git_sha": "5c460c5a4736974abde2843294f35307ee2b0e5e",
+                        "git_sha": "e06548bfa36ee31869b81041879dd6b3a83b1d57",
+                        "installed_by": ["modules"]
+                    },
+                    "minimap2/align": {
+                        "branch": "master",
+                        "git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220",
                         "installed_by": ["modules"]
                     },
                     "mosdepth": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "ebb27711cd5f4de921244bfa81c676504072d31c",
                         "installed_by": ["modules"]
                     },
                     "multiqc": {
+                        "branch": "master",
+                        "git_sha": "a6e11ac655e744f7ebc724be669dd568ffdc0e80",
+                        "installed_by": ["modules"]
+                    },
+                    "samtools/fasta": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     },
-                    "samtools/view": {
+                    "samtools/index": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
+                    },
+                    "samtools/view": {
+                        "branch": "master",
+                        "git_sha": "3ffae3598260a99e8db3207dead9f73f87f90d1f",
+                        "installed_by": ["modules"]
                     }
                 }
             },