Fix merging discrepancies

sanger-tol · Oct 6, 2023 · 06e304e · 06e304e
1 parent 57beb02
commit 06e304e
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Showing 4 changed files with 148 additions and 39 deletions.
diff --git a/assets/test_iyVesGerm1.yaml b/assets/test_iyVesGerm1.yaml
@@ -1,21 +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
-    mito:
-      species: Vespula germanica
-      min_length: 15000
-      code: 5
+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
diff --git a/modules.json b/modules.json
@@ -140,11 +140,6 @@
                         "git_sha": "02c3c39e3d57bf77183e563598bae2ec1ec11cb1",
                         "installed_by": ["modules"]
                     },
-                    "multiqc": {
-                        "branch": "master",
-                        "git_sha": "ee80d14721e76e2e079103b8dcd5d57129e584ba",
-                        "installed_by": ["modules"]
-                    },
                     "pretextmap": {
                         "branch": "master",
                         "git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b",

diff --git a/modules/local/mitohifi.nf → modules/nf-core/mitohifi/mitohifi/main.nf b/modules/local/mitohifi.nf → modules/nf-core/mitohifi/mitohifi/main.nf
diff --git a/modules/nf-core/mitohifi/mitohifi/meta.yml b/modules/nf-core/mitohifi/mitohifi/meta.yml