Merge pull request #21 from DLBPointon/generate_genome

Generate genome

modules.json

@@ -17,6 +17,9 @@
             },
             "minimap2/align": {
                 "git_sha": "1a5a9e7b4009dcf34e6867dd1a5a1d9a718b027b"
+            },
+            "samtools/faidx": {
+                "git_sha": "ce06694af8ca2f7453206aa974c2c9a2b99ec093"
             }
         }
     }

modules/local/generate_genome_file.nf

@@ -0,0 +1,15 @@
+process GENERATE_GENOME_FILE {
+    tag "${meta}"
+    label "process_small"
+
+    input:
+    tuple val( meta ), path( fai )
+
+    output:
+    tuple val( meta ), file( "my.genome" ),     emit: dotgenome
+
+    script:
+    """
+    cut -f1,2 $fai | sort -k2,2 -nr > my.genome
+    """
+}

subworkflows/local/generate_genome.nf

@@ -0,0 +1,18 @@
+include { SAMTOOLS_FAIDX        } from '../../modules/nf-core/modules/samtools/faidx/main'
+include { GENERATE_GENOME_FILE  } from '../../modules/local/genome_file_generator'
+
+workflow GENERATE_GENOME {
+    main:
+    ch_versions     = Channel.empty()
+
+    SAMTOOLS_FAIDX ( [[params.assembly.sample], params.reference] )
+    ch_versions     = ch_versions.mix(SAMTOOLS_FAIDX.out.versions)
+
+    GENERATE_GENOME_FILE ( SAMTOOLS_FAIDX.out.fai )
+
+    emit:
+    dot_genome      = GENERATE_GENOME_FILE.out.dotgenome
+
+    versions        = ch_versions.ifEmpty(null)
+
+}

workflows/treeval.nf

@@ -11,7 +11,7 @@ WorkflowTreeval.initialise(params, log)
 
 // TODO nf-core: Add all file path parameters for the pipeline to the list below
 // Check input path parameters to see if they exist
-def checkPathParamList = [ params.input, params.multiqc_config, params.fasta ]
+def checkPathParamList = [ params.fasta ]
 for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true) } }
 
 // Check mandatory parameters
@@ -27,7 +27,7 @@ if (params.input) { ch_input = file(params.input) } else { exit 1, 'Input sample
 //
 // SUBWORKFLOW: Consisting of a mix of local and nf-core/modules
 //
-include { INPUT_CHECK } from '../subworkflows/local/input_check'
+include { GENERATE_GENOME   } from '../subworkflows/local/generate_genome'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -38,7 +38,6 @@ include { INPUT_CHECK } from '../subworkflows/local/input_check'
 //
 // MODULE: Installed directly from nf-core/modules
 //
-
 include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/modules/custom/dumpsoftwareversions/main'
 
 /*
@@ -54,14 +53,10 @@ workflow TREEVAL {
 
     ch_versions = Channel.empty()
 
-    //
-    // SUBWORKFLOW: Read in samplesheet, validate and stage input files
-    //
-    INPUT_CHECK (
-        ch_input
-    )
-    ch_versions = ch_versions.mix(INPUT_CHECK.out.versions)
+    GENERATE_GENOME ()
+    ch_versions = ch_versions.mix(GENERATE_GENOME.out.versions)
 
+    // TO PASS .genome INTO SUBWORKFLOW add `GENERATE_GENOME.out.dot_genome`
 
     CUSTOM_DUMPSOFTWAREVERSIONS (
         ch_versions.unique().collectFile(name: 'collated_versions.yml')