Update pipeline to use MIXED_INPUT

modules/validate.nf

@@ -1,3 +1,41 @@
+// Map of valid parameters for which to skip validation
+skipValidationParams = [
+    // From common config
+    input: 'skip',
+    tracedir: 'skip',
+    max_memory: 'skip',
+    max_cpus: 'skip',
+    max_time: 'skip',
+    max_retries: 'skip',
+    retry_strategy: 'skip',
+    queue_size: 'skip',
+    submit_rate_limit: 'skip',
+    // From mixed input config
+    outdir: 'skip',
+    manifest_of_reads: 'skip',
+    manifest_of_lanes: 'skip',
+    manifest: 'skip',
+    save_metadata: 'skip',
+    combine_same_id_crams: 'skip',
+    dehumanising_method: 'skip',
+    cleanup_intermediate_files_irods_extractor: 'skip',
+    save_fastqs: 'skip',
+    save_method: 'skip',
+    raw_reads_prefix: 'skip',
+    preexisting_fastq_tag: 'skip',
+    split_sep_for_ID_from_fastq: 'skip',
+    lane_plex_sep: 'skip',
+    start_queue: 'skip',
+    irods_subset_to_skip: 'skip',
+    short_metacsv_name: 'skip',
+    studyid: 'skip',
+    runid: 'skip',
+    laneid: 'skip',
+    plexid: 'skip',
+    target: 'skip',
+    type: 'skip'
+] 
+
 // Map of valid parameters and their value types
 validParams = [
     help: 'boolean',
@@ -31,6 +69,8 @@ validParams = [
     lite: 'boolean'
 ]
 
+validParams += skipValidationParams
+
 // Validate whether all provided parameters are valid
 void validate(Map params) {
     // Ensure only one or none of the alternative workflows is selected

nextflow.config

@@ -1,5 +1,10 @@
 nextflow.enable.dsl=2
 
+// Import mixed input params
+includeConfig "https://raw.githubusercontent.com/sanger-pathogens/nextflow-commons/cb60d523f202dace1b1efd02a5ae03f8a4b049a6/configs/nextflow.config"
+includeConfig "$projectDir/assorted-sub-workflows/irods_extractor/subworkflows/irods.config"
+includeConfig "$projectDir/assorted-sub-workflows/mixed_input/subworkflows/mixed_input.config"
+
 // Default parameters that can be overridden
 params {
     // Show help message
@@ -13,6 +18,8 @@ params {
     reads = "$projectDir/input"
     // Default output directory
     output = "$projectDir/output"
+    // To allow mixed input to work without warnings
+    outdir = output
 
     // Default databases directory for saving all the required databases
     db = "$projectDir/databases"
@@ -63,8 +70,11 @@ params {
     lite = false
 }
 
-// Set auto-retry and process container images
 process {
+    // Avoid use of `-o pipefail` as this fails version info collation
+    shell = ['/bin/bash', '-eu']
+
+    // Set auto-retry and process container images
     maxRetries = 2
     errorStrategy = { task.attempt <= process.maxRetries ? 'retry' : 'ignore' }
 
@@ -192,4 +202,10 @@ profiles {
         }
     }
 
+    // Profile for Sanger
+    sanger {
+        singularity {
+            runOptions = '--bind /lustre,/nfs,/data,/software,/tmp'
+        }
+    }
 }

workflows/pipeline.nf

@@ -10,6 +10,9 @@ include { MLST } from "$projectDir/modules/mlst"
 include { PBP_RESISTANCE; PARSE_PBP_RESISTANCE; GET_ARIBA_DB; OTHER_RESISTANCE; PARSE_OTHER_RESISTANCE } from "$projectDir/modules/amr"
 include { GENERATE_SAMPLE_REPORT; GENERATE_OVERALL_REPORT } from "$projectDir/modules/output"
 
+// Import subworkflows
+include { MIXED_INPUT } from "$projectDir/assorted-sub-workflows/mixed_input/mixed_input"
+
 // Main pipeline workflow
 workflow PIPELINE {
     main:
@@ -29,8 +32,17 @@ workflow PIPELINE {
     // Get path to ARIBA database, generate from reference sequences and metadata if ncessary
     GET_ARIBA_DB(params.ariba_ref, params.ariba_metadata, params.db)
 
+    // Obtain input from manifests and iRODS params
+    MIXED_INPUT
+    | map { meta, R1, R2 -> [meta.ID, [R1, R2]] }
+    | set { raw_read_pairs_ch }
+
     // Get read pairs into Channel raw_read_pairs_ch
-    raw_read_pairs_ch = Channel.fromFilePairs("$params.reads/*_{,R}{1,2}{,_001}.{fq,fastq}{,.gz}", checkIfExists: true)
+    if (params.reads) {
+        Channel.fromFilePairs("$params.reads/*_{,R}{1,2}{,_001}.{fq,fastq}{,.gz}", checkIfExists: true)
+        | mix(raw_read_pairs_ch)
+        | set { raw_read_pairs_ch }
+    }
 
     // Basic input files validation
     // Output into Channel FILE_VALIDATION.out.result