From d4336a1c31e04a5110fda034ee9bff2428821bb3 Mon Sep 17 00:00:00 2001
From: Ksenia Krasheninnikova <kk16@sanger.ac.uk>
Date: Wed, 4 Oct 2023 14:28:06 +0100
Subject: [PATCH] Lint and prettify

---
 assets/test.yaml            |   2 +-
 assets/test_gsMetZobe1.yaml |  22 +++--
 modules.json                | 190 +++++++++---------------------------
 3 files changed, 62 insertions(+), 152 deletions(-)

diff --git a/assets/test.yaml b/assets/test.yaml
index d1ee78ee..e4562bf7 100644
--- a/assets/test.yaml
+++ b/assets/test.yaml
@@ -14,4 +14,4 @@ busco:
 mito:
   species: Caradrina clavipalpis
   min_length: 15000
-  code: 5
\ No newline at end of file
+  code: 5
diff --git a/assets/test_gsMetZobe1.yaml b/assets/test_gsMetZobe1.yaml
index 647205a9..c2bd4ab7 100644
--- a/assets/test_gsMetZobe1.yaml
+++ b/assets/test_gsMetZobe1.yaml
@@ -1,14 +1,18 @@
 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
+  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
diff --git a/modules.json b/modules.json
index 6dca0e40..aaf81f44 100644
--- a/modules.json
+++ b/modules.json
@@ -8,341 +8,247 @@
                     "bcftools/concat": {
                         "branch": "master",
                         "git_sha": "582ff1755bdd205c65e2ba4c31e0a008dae299ec",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "bcftools/consensus": {
                         "branch": "master",
                         "git_sha": "fa12afdf5874c1d11e4a20efe81c97935e8eea24",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "bcftools/index": {
                         "branch": "master",
                         "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "bcftools/norm": {
                         "branch": "master",
                         "git_sha": "0435e4eebc94e53721c194b2d5d06f455a79e407",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "bcftools/sort": {
                         "branch": "master",
                         "git_sha": "4a21e4cca35e72ec059abd67f790e0b192ce5d81",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "bcftools/view": {
                         "branch": "master",
                         "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "bedtools/bamtobed": {
                         "branch": "master",
                         "git_sha": "9e51255c4f8ec69fb6ccf68593392835f14fecb8",
-                        "installed_by": [
-                            "modules"
-                        ],
+                        "installed_by": ["modules"],
                         "patch": "modules/nf-core/bedtools/bamtobed/bedtools-bamtobed.diff"
                     },
                     "busco": {
                         "branch": "master",
                         "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "bwamem2/index": {
                         "branch": "master",
                         "git_sha": "bfed129da5134b4439b1821c917972570d44d39c",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "cat/cat": {
                         "branch": "master",
                         "git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "cooler/cload": {
                         "branch": "master",
                         "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "cooler/zoomify": {
                         "branch": "master",
                         "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
                         "git_sha": "76cc4938c1f6ea5c7d83fed1eeffc146787f9543",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "fastk/fastk": {
                         "branch": "master",
                         "git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "fastk/histex": {
                         "branch": "master",
                         "git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "fastqc": {
                         "branch": "master",
                         "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "freebayes": {
                         "branch": "master",
                         "git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b",
-                        "installed_by": [
-                            "modules"
-                        ],
+                        "installed_by": ["modules"],
                         "patch": "modules/nf-core/freebayes/freebayes.diff"
                     },
                     "gatk4/mergevcfs": {
                         "branch": "master",
                         "git_sha": "643756685546fa61f5c8fba439af746c090b9180",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "genescopefk": {
                         "branch": "master",
                         "git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "gfastats": {
                         "branch": "master",
                         "git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b",
-                        "installed_by": [
-                            "modules"
-                        ],
+                        "installed_by": ["modules"],
                         "patch": "modules/nf-core/gfastats/gfastats.diff"
                     },
                     "gunzip": {
                         "branch": "master",
                         "git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "hifiasm": {
                         "branch": "master",
                         "git_sha": "07b737b47d33d8d980e5e0c09736764f450980a3",
-                        "installed_by": [
-                            "modules"
-                        ],
+                        "installed_by": ["modules"],
                         "patch": "modules/nf-core/hifiasm/hifiasm.diff"
                     },
                     "merquryfk/merquryfk": {
                         "branch": "master",
                         "git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "minimap2/align": {
                         "branch": "master",
                         "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
-                        "installed_by": [
-                            "modules"
-                        ],
+                        "installed_by": ["modules"],
                         "patch": "modules/nf-core/minimap2/align/minimap2-align.diff"
                     },
                     "mitohifi/findmitoreference": {
                         "branch": "master",
                         "git_sha": "f52220e84bfc16a8616a5bb3d6f5bc67d601bdce",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "mitohifi/mitohifi": {
                         "branch": "master",
                         "git_sha": "02c3c39e3d57bf77183e563598bae2ec1ec11cb1",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "multiqc": {
                         "branch": "master",
                         "git_sha": "ee80d14721e76e2e079103b8dcd5d57129e584ba",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "pretextmap": {
                         "branch": "master",
                         "git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "pretextsnapshot": {
                         "branch": "master",
                         "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "purgedups/calcuts": {
                         "branch": "master",
                         "git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b",
-                        "installed_by": [
-                            "modules"
-                        ],
+                        "installed_by": ["modules"],
                         "patch": "modules/nf-core/purgedups/calcuts/purgedups-calcuts.diff"
                     },
                     "purgedups/getseqs": {
                         "branch": "master",
                         "git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "purgedups/pbcstat": {
                         "branch": "master",
                         "git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "purgedups/purgedups": {
                         "branch": "master",
                         "git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "purgedups/splitfa": {
                         "branch": "master",
                         "git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "samtools/collate": {
                         "branch": "master",
                         "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "samtools/faidx": {
                         "branch": "master",
                         "git_sha": "fd742419940e01ba1c5ecb172c3e32ec840662fe",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "samtools/fixmate": {
                         "branch": "master",
                         "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "samtools/flagstat": {
                         "branch": "master",
                         "git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "samtools/idxstats": {
                         "branch": "master",
                         "git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "samtools/index": {
                         "branch": "master",
                         "git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "samtools/markdup": {
                         "branch": "master",
                         "git_sha": "9e51255c4f8ec69fb6ccf68593392835f14fecb8",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "samtools/merge": {
                         "branch": "master",
                         "git_sha": "0460d316170f75f323111b4a2c0a2989f0c32013",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "samtools/sort": {
                         "branch": "master",
                         "git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "samtools/stats": {
                         "branch": "master",
                         "git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "samtools/view": {
                         "branch": "master",
                         "git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "seqtk/subseq": {
                         "branch": "master",
                         "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
-                        "installed_by": [
-                            "modules"
-                        ],
+                        "installed_by": ["modules"],
                         "patch": "modules/nf-core/seqtk/subseq/seqtk-subseq.diff"
                     },
                     "yahs": {
                         "branch": "master",
                         "git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     }
                 }
             }
         }
     }
-}
\ No newline at end of file
+}