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Update all modules (#126)
* bump modules * fix workflow to adjust to updated modules * pre-commit * fix repeat flow + more shards * fix tests * sort order of callers in VCF + fix test
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Lines changed: 5041 additions & 2497 deletions

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‎.github/workflows/nf-test.yml‎

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Original file line numberDiff line numberDiff line change
@@ -49,7 +49,7 @@ jobs:
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env:
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NFT_VER: ${{ env.NFT_VER }}
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with:
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max_shards: 7
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max_shards: 14
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- name: debug
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run: |

‎bin/fix_callers.py‎

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@@ -31,10 +31,9 @@ def process_file(file, output) -> None:
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for field in info.split(";"):
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split_field = field.split("=", 1)
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key, value = (split_field[0], split_field[1]) if len(split_field) == 2 else (split_field[0], "")
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print(key, value)
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info_dict[key] = value
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info_dict["CALLERS"] = ",".join(set([it.split("_")[0] for it in info_dict["IDLIST_EXT"].replace(".", ",").split(",")]))
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info_dict["CALLERS"] = ",".join(sorted(set([it.split("_")[0] for it in info_dict["IDLIST_EXT"].replace(".", ",").split(",")])))
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if len(info_dict["CALLERS"]) == 0:
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del info_dict["CALLERS"]
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out_file.write(f"{pre_info}\t{';'.join([f'{key}={value}' for key, value in info_dict.items()])}\t{after_info}")

‎modules.json‎

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Original file line numberDiff line numberDiff line change
@@ -7,69 +7,68 @@
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"nf-core": {
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"bcftools/annotate": {
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"branch": "master",
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"git_sha": "2ad29c2aed06d815d9f68ad7ba20b3b1c574ce9c",
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"installed_by": ["modules"],
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"patch": "modules/nf-core/bcftools/annotate/bcftools-annotate.diff"
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"git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
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"installed_by": ["modules"]
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},
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"bcftools/concat": {
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"branch": "master",
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"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
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"git_sha": "345b60fff6a192d55c2a220ae413c57f29b698b7",
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"installed_by": ["modules"]
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},
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"bcftools/filter": {
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"branch": "master",
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"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
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"git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
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"installed_by": ["modules"]
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},
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"bcftools/sort": {
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"branch": "master",
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"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
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"git_sha": "1a2aa4aaf1916cca388cf27c7a6d8238bb5ad68b",
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"installed_by": ["modules"]
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},
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"bedgovcf": {
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"branch": "master",
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"git_sha": "71a96063a7e09be7ea48f069d134a56ce86c9ba6",
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"git_sha": "5cb9a8694da0a0e550921636bb60bc8c56445fd7",
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"installed_by": ["modules"]
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},
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"bwa/index": {
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"branch": "master",
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"git_sha": "2d20463181b1c38981a02e90d3084b5f9fa8d540",
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"git_sha": "1c46359c837ef768b004519f535c30378e8289fc",
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"installed_by": ["modules"]
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},
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"delly/call": {
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"branch": "master",
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"git_sha": "699f066b2d90f079378205ce557f9ea75d90dbf9",
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"git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
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"installed_by": ["modules"]
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},
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"ensemblvep/download": {
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"branch": "master",
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"git_sha": "f9234d35f5b9143313a4773fb54716876c030323",
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"git_sha": "f50d3c606dbc7e5af367cce070d824b796872ed2",
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"installed_by": ["modules"]
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},
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"ensemblvep/vep": {
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"branch": "master",
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"git_sha": "f9234d35f5b9143313a4773fb54716876c030323",
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"git_sha": "f50d3c606dbc7e5af367cce070d824b796872ed2",
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"installed_by": ["modules"]
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},
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"expansionhunter": {
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"branch": "master",
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"git_sha": "b42fec6f7c6e5d0716685cabb825ef6bf6e386b5",
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"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
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"installed_by": ["modules"],
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"patch": "modules/nf-core/expansionhunter/expansionhunter.diff"
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},
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"gatk4/createsequencedictionary": {
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"branch": "master",
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"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
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"git_sha": "ae8cd884f895585c6799ab4eb6a2c9f44df03336",
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"installed_by": ["modules"]
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},
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"gatk4/svannotate": {
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"branch": "master",
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"git_sha": "a57253204b8f4022edfeaa3ae2f5e2abecd8858b",
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"git_sha": "ae8cd884f895585c6799ab4eb6a2c9f44df03336",
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"installed_by": ["modules"]
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},
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"gawk": {
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"branch": "master",
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"git_sha": "b42fec6f7c6e5d0716685cabb825ef6bf6e386b5",
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"git_sha": "5ee4d69ed992c3ce81cfbbdd0bef932fcb81c75a",
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"installed_by": ["modules"]
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},
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"jasminesv": {
@@ -89,51 +88,49 @@
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},
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"multiqc": {
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"branch": "master",
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"git_sha": "9656d955b700a8707c4a67821ab056f8c1095675",
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"git_sha": "80cba9452fb1e9bb79884976fa1ca0e671949aa2",
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"installed_by": ["modules"]
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},
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"ngsbits/samplegender": {
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"branch": "master",
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"git_sha": "0e9cb409c32d3ec4f0d3804588e4778971c09b7e",
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"git_sha": "ae8668d026462283f3bdc70ad2d6c78f8919fe68",
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"installed_by": ["modules"]
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},
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"samtools/convert": {
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"branch": "master",
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"git_sha": "b42fec6f7c6e5d0716685cabb825ef6bf6e386b5",
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"git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
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"installed_by": ["modules"],
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"patch": "modules/nf-core/samtools/convert/samtools-convert.diff"
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},
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"samtools/faidx": {
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"branch": "master",
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"git_sha": "f153f1f10e1083c49935565844cccb7453021682",
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"git_sha": "9a48bce39a67e2cb34b8f125fc1d50f0ad98b616",
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"installed_by": ["modules"]
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},
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"samtools/index": {
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"branch": "master",
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"git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62",
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"git_sha": "c8be52dba1166c678e74cda9c3a3c221635c8bb1",
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"installed_by": ["modules"]
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},
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"samtools/merge": {
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"branch": "master",
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"git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62",
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"git_sha": "9a48bce39a67e2cb34b8f125fc1d50f0ad98b616",
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"installed_by": ["modules"]
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},
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"smoove/call": {
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"branch": "master",
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"git_sha": "f2fdc5e81efe36beff213752ce1a8e71fceeacba",
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"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
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"installed_by": ["modules"]
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},
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"strvctvre/strvctvre": {
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"branch": "master",
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"git_sha": "e05456babfdf276f4771b140d04fb41eb2a2d13c",
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"installed_by": ["modules"],
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"patch": "modules/nf-core/strvctvre/strvctvre/strvctvre-strvctvre.diff"
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"git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
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"installed_by": ["modules"]
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},
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"svtools/vcftobedpe": {
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"branch": "master",
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"git_sha": "5cf15e4c5ad6d06718b35e5ec1655c7c0a105880",
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"installed_by": ["modules"],
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"patch": "modules/nf-core/svtools/vcftobedpe/svtools-vcftobedpe.diff"
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"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
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"installed_by": ["modules"]
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},
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"svync": {
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"branch": "master",
@@ -142,33 +139,32 @@
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},
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"tabix/bgziptabix": {
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"branch": "master",
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"git_sha": "09d3c8c29b31a2dfd610305b10550f0e1dbcd4a9",
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"git_sha": "61846a0d757ff9c0682ba3e28ab0441afd95ad7e",
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"installed_by": ["modules"]
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},
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"tabix/tabix": {
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"branch": "master",
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"git_sha": "9502adb23c0b97ed8e616bbbdfa73b4585aec9a1",
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"git_sha": "524a7d5ef99a0cbfb4feec8bf7062eb6a531931a",
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"installed_by": ["modules"]
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},
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"untar": {
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"branch": "master",
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"git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
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"git_sha": "00ee87ebb541af0008596400ce6d5f66d79d5408",
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"installed_by": ["modules"]
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},
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"vcfanno": {
159156
"branch": "master",
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"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
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"installed_by": ["modules"],
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"patch": "modules/nf-core/vcfanno/vcfanno.diff"
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"git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
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"installed_by": ["modules"]
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},
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"wisecondorx/convert": {
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"branch": "master",
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"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
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"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
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"installed_by": ["modules"]
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},
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"wisecondorx/predict": {
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"branch": "master",
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"git_sha": "c3a2705bff298ffd2972bdb1b925b362491e2ee3",
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"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
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"installed_by": ["modules"]
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}
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}

‎modules/nf-core/bcftools/annotate/bcftools-annotate.diff‎

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‎modules/nf-core/bcftools/annotate/environment.yml‎

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‎modules/nf-core/bcftools/annotate/main.nf‎

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