Subworkflow for organelles

assets/test.yaml

@@ -11,3 +11,7 @@ dataset:
 hic_motif: GATC,GANTC,CTNAG,TTAA
 busco:
   lineage: bacteria_odb10
+mito:
+  species: Caradrina clavipalpis
+  min_length: 15000
+  code: 5

assets/test_gsMetZobe1.yaml

@@ -1,14 +1,18 @@
-samples:
-  - id: gsMetZobe1
-    illumina_10X:
-      reads: /lustre/scratch124/tol/projects/darwin/users/kk16/development/nextflow/gsMetZobe1/10x/
-    pacbio:
-      reads:
-        - reads: /lustre/scratch124/tol/projects/darwin/users/kk16/development/nextflow/gsMetZobe1/pacbio/m64125_200823_145825.ccs.bc1019_BAK8B_OA--bc1019_BAK8B_OA.filtered.fasta.gz
-    HiC:
-      reads:
-        - reads: /lustre/scratch124/tol/projects/darwin/users/kk16/development/nextflow/gsMetZobe1/hic-arima/35528_4#7.cram
-arima_motif: GATC,GANTC,CTNAG,TTAA
+dataset:
+  id: gsMetZobe1
+  illumina_10X:
+    reads: /lustre/scratch124/tol/projects/darwin/users/kk16/development/nextflow/gsMetZobe1/10x/
+  pacbio:
+    reads:
+      - reads: /lustre/scratch124/tol/projects/darwin/users/kk16/development/nextflow/gsMetZobe1/pacbio/m64125_200823_145825.ccs.bc1019_BAK8B_OA--bc1019_BAK8B_OA.filtered.fasta.gz
+  HiC:
+    reads:
+      - reads: /lustre/scratch124/tol/projects/darwin/users/kk16/development/nextflow/gsMetZobe1/hic-arima/35528_4#7.cram
+hic_motif: GATC,GANTC,CTNAG,TTAA
 busco:
   lineages_path: /lustre/scratch123/tol/resources/busco/v5/
   lineage: fungi_odb10
+mito:
+  species: Metschnikowia zobellii
+  min_length: 15000
+  code: 4

assets/test_iyVesGerm1.yaml

@@ -1,17 +1,18 @@
-samples:
-  - id: iyVesGerm1
-    assembly:
-      primary: /lustre/scratch124/tol/projects/darwin/data/insects/Vespula_germanica/working/iyVesGerm1.hifiasm.20201015/iyVesGerm1.p_ctg.fa.gz
-      haplotigs: /lustre/scratch124/tol/projects/darwin/data/insects/Vespula_germanica/working/iyVesGerm1.hifiasm.20201015/iyVesGerm1.a_ctg.fa.gz
-    illumina_10X:
-      reads: /lustre/scratch124/tol/projects/darwin/users/kk16/development/nextflow/sanger-tol-genomeassembly/test/10X_iyVesGerm1
-    pacbio:
-      reads:
-        - reads: /lustre/scratch124/tol/projects/darwin/data/insects/Vespula_germanica/genomic_data/iyVesGerm1/pacbio/fasta/m64094_200217_145414.ccs.bc1011_BAK8A_OA--bc1011_BAK8A_OA.filtered.fasta.gz
-    HiC:
-      reads:
-        - reads: /lustre/scratch124/tol/projects/darwin/data/insects/Vespula_germanica/genomic_data/iyVesGerm1/hic-arima2/34957_3#2.cram
-      arima_motif: GATC,GANTC,CTNAG,TTAA
-    busco:
-      lineages_path: /lustre/scratch123/tol/resources/busco/v5/
-      lineage: insecta_odb10
+dataset:
+  id: iyVesGerm1
+  illumina_10X:
+    reads: /lustre/scratch124/tol/projects/darwin/users/kk16/development/nextflow/sanger-tol-genomeassembly/test/10X_iyVesGerm1
+  pacbio:
+    reads:
+      - reads: /lustre/scratch124/tol/projects/darwin/data/insects/Vespula_germanica/genomic_data/iyVesGerm1/pacbio/fasta/m64094_200217_145414.ccs.bc1011_BAK8A_OA--bc1011_BAK8A_OA.filtered.fasta.gz
+  HiC:
+    reads:
+      - reads: /lustre/scratch124/tol/projects/darwin/data/insects/Vespula_germanica/genomic_data/iyVesGerm1/hic-arima2/34957_3#2.cram
+hic_motif: GATC,GANTC,CTNAG,TTAA
+busco:
+  lineages_path: /lustre/scratch123/tol/resources/busco/v5/
+  lineage: insecta_odb10
+mito:
+  species: Vespula germanica
+  min_length: 15000
+  code: 5

conf/modules.config

@@ -172,6 +172,25 @@ process {
     }
     // End of Set up of the raw assembly pipeline
 
+    // Set up of organelles pipeline
+
+    withName: '.*ORGANELLES:MITOHIFI_MITOHIFI_READS' {
+        publishDir = [
+            path: { "${params.outdir}/${meta.id}.${params.hifiasm}/mito.reads" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+    withName: '.*ORGANELLES:MITOHIFI_MITOHIFI_ASM' {
+        publishDir = [
+            path: { "${params.outdir}/${meta.id}.${params.hifiasm}/mito" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+    // End of set up of organelles pipeline
+
     // Set up of the purging pipeline
 
     withName: '.*PURGE_DUPS_PRI:MINIMAP2_ALIGN_READS' {

modules.json

@@ -130,6 +130,16 @@
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/minimap2/align/minimap2-align.diff"
                     },
+                    "mitohifi/findmitoreference": {
+                        "branch": "master",
+                        "git_sha": "f52220e84bfc16a8616a5bb3d6f5bc67d601bdce",
+                        "installed_by": ["modules"]
+                    },
+                    "mitohifi/mitohifi": {
+                        "branch": "master",
+                        "git_sha": "02c3c39e3d57bf77183e563598bae2ec1ec11cb1",
+                        "installed_by": ["modules"]
+                    },
                     "pretextmap": {
                         "branch": "master",
                         "git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b",