add stitch tool

conf/test_stitch.config

@@ -0,0 +1,33 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    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 nf-core/phaseimpute -profile test_stitch,<docker/singularity> --outdir <OUTDIR>
+
+----------------------------------------------------------------------------------------
+*/
+
+params {
+    config_profile_name        = 'Minimal Stitch Test profile'
+    config_profile_description = 'Minimal test dataset to check pipeline function using the tool STITCH'
+
+    // Limit resources so that this can run on GitHub Actions
+    max_cpus   = 2
+    max_memory = '2.GB'
+    max_time   = '1.h'
+
+    // Input data
+    input        = "${projectDir}/tests/csv/sample_bam.csv"
+    input_region = "${projectDir}/tests/csv/region.csv"
+
+    // Genome references
+    fasta  = "https://raw.githubusercontent.com/nf-core/test-datasets/phaseimpute/data/reference_genome/21_22/hs38DH.chr21_22.fa"
+    phased = true
+
+    // Impute parameters
+    step   = "impute"
+    tools  = "stitch"
+}

modules.json

@@ -156,6 +156,11 @@
                         "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["vcf_phase_shapeit5"]
                     },
+                    "stitch": {
+                        "branch": "master",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "installed_by": ["modules"]
+                    },
                     "tabix/bgzip": {
                         "branch": "master",
                         "git_sha": "09d3c8c29b31a2dfd610305b10550f0e1dbcd4a9",

nextflow.config

@@ -199,12 +199,14 @@ profiles {
         executor.memory        = 8.GB
     }
 
-    test          { includeConfig 'conf/test.config'          }
-    test_full     { includeConfig 'conf/test_full.config'     }
-    test_sim      { includeConfig 'conf/test_sim.config'      }
+    test        { includeConfig 'conf/test.config'          }
+    test_full   { includeConfig 'conf/test_full.config'     }
+    test_sim    { includeConfig 'conf/test_sim.config'      }
     test_validate { includeConfig 'conf/test_validate.config' }
     test_all      { includeConfig 'conf/test_all.config'      }
-    test_quilt { includeConfig 'conf/test_quilt.config'  }
+    test_quilt  { includeConfig 'conf/test_quilt.config'    }
+    test_stitch { includeConfig 'conf/test_stitch.config'   }
+
 }
 
 // Set default registry for Apptainer, Docker, Podman and Singularity independent of -profile

nextflow_schema.json

@@ -144,7 +144,7 @@
                     "type": "string",
                     "description": "Step to run.",
                     "fa_icon": "fas fa-step-forward",
-                    "enum": ["glimpse1", "glimpse2", "quilt"]
+                    "enum": ["glimpse1", "glimpse2", "quilt", "stitch"]
                 }
             }
         },

subworkflows/local/bam_impute_stitch/bam_impute_stitch.nf

@@ -0,0 +1,28 @@
+include { BCFTOOLS_QUERY     } from '../../../modules/nf-core/bcftools/query/main'
+include { STITCH             } from '../../../modules/nf-core/stitch/main'
+
+workflow BAM_IMPUTE_STITCH {
+
+    take:
+    ch_input                                 //  channel: [ val(meta), bam, bai ]
+    ch_panel_sites
+
+    main:
+
+    ch_versions      = Channel.empty()
+
+    // Convert position file to tab-separated file
+    BCFTOOLS_QUERY(ch_panel_sites)
+    ch_posfile = BCFTOOLS_QUERY.out.output
+
+
+    // Run STITCH
+    STITCH( stitch_input, GET_READS.out, reference, seed )
+
+
+
+    emit:
+    ch_vcf_tbi                                                          // channel:  [ meta, vcf, tbi ]
+    versions                   = ch_versions                           // channel:   [ versions.yml ]
+
+}

workflows/phaseimpute/main.nf

@@ -169,8 +169,33 @@ workflow PHASEIMPUTE {
                 error "Glimpse2 not yet implemented"
                 // Glimpse2 subworkflow
             }
+
+            if (params.tools.contains("stitch")) {
+                print("Impute with STITCH")
+                // STITCH subworkflow
+
+                // Make bamlist from bam input
+                ch_bamlist = ch_input
+                            .map { it[1].tokenize('/').last() }
+                            .collectFile( name: "bamlist.txt", newLine: true, sort: true )
+
+                // Get chromosomes
+                ch_chromosomes = ch_fasta.map{it -> it[2]}
+                .splitCsv(header: ["chr", "size", "offset", "lidebase", "linewidth", "qualoffset"], sep: "\t")
+                .map{it -> [chr:it.chr]}
+
+                ch_chromosomes.dump(tag:"ch_chromosomes")
+
+                // Prepare input for STITCH
+
+                // Impute with STITCH
+                //BAM_IMPUTE_STITCH ( ch_input_stitch, GET_PANEL.out.ch_panel_sites )
+
+
+            }
+
             if (params.tools.contains("quilt")) {
-                print("Impute with quilt")
+                print("Impute with QUILT")
 
                 // Quilt subworkflow