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maxulyssemaxulysse
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update all modules (#124)
* update all modules * update sarek references * fix linting
1 parent 22de15c commit b497e20

66 files changed

Lines changed: 770 additions & 1265 deletions

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‎main.nf‎

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@@ -274,7 +274,10 @@ workflow NFCORE_REFERENCES {
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// Mix the references that were extracted with the references that did not need to be extracted
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// Some references are not extracted because they are usually not stored in an archived format
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// TODO: check if more references need to be extracted
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altliftoverfile = Channel.empty()
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REFERENCES(
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altliftoverfile,
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ascat_alleles_input.not_extracted.mix(extracted_reference.ascat_alleles),
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ascat_loci_input.not_extracted.mix(extracted_reference.ascat_loci),
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ascat_loci_gc_input.not_extracted.mix(extracted_reference.ascat_loci_gc),

‎modules.json‎

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@@ -5,39 +5,24 @@
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"https://github.com/nf-core/modules.git": {
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"modules": {
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"nf-core": {
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"bbmap/bbsplit": {
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"branch": "master",
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"git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
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"installed_by": ["modules"]
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},
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"custom/catadditionalfasta": {
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"branch": "master",
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"git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
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"installed_by": ["modules"]
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},
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"gunzip": {
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"branch": "master",
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"git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
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"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
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"installed_by": ["archive_extract"]
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},
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"multiqc": {
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"branch": "master",
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"git_sha": "c9a31c472ef2d86802eb44f27322955849859361",
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"installed_by": ["modules"]
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},
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"sortmerna": {
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"branch": "master",
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"git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
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"git_sha": "a4488d3d09244f29fb4606ba4eef85d59dcc6ad8",
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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": "05954dab2ff481bcb999f24455da29a5828af08d",
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"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
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"installed_by": ["archive_extract"]
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},
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"unzip": {
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"branch": "master",
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"git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
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"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
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"installed_by": ["archive_extract"]
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}
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}
@@ -51,17 +36,17 @@
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},
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"utils_nextflow_pipeline": {
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"branch": "master",
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"git_sha": "c2b22d85f30a706a3073387f30380704fcae013b",
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"git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
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"installed_by": ["subworkflows"]
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},
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"utils_nfcore_pipeline": {
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"branch": "master",
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"git_sha": "51ae5406a030d4da1e49e4dab49756844fdd6c7a",
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"git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
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"installed_by": ["subworkflows"]
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},
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"utils_nfschema_plugin": {
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"branch": "master",
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"git_sha": "2fd2cd6d0e7b273747f32e465fdc6bcc3ae0814e",
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"git_sha": "dcd088f483cede0c3df4034d405126f05a764cc7",
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"installed_by": ["subworkflows"]
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}
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}
@@ -72,92 +57,97 @@
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"nf-side": {
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"bowtie/build": {
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"branch": "main",
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"git_sha": "4d329b41d14a20dec31cae811f39e1a52b435220",
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"git_sha": "5c580db443878c702f9ec63c62c18951fe06ab0a",
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"installed_by": ["prepare_genome_rnaseq"]
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},
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"bowtie2/build": {
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"branch": "main",
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"git_sha": "4d329b41d14a20dec31cae811f39e1a52b435220",
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"git_sha": "5c580db443878c702f9ec63c62c18951fe06ab0a",
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"installed_by": ["prepare_genome_rnaseq"]
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},
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"bwa/index": {
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"branch": "main",
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"git_sha": "4d329b41d14a20dec31cae811f39e1a52b435220",
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"git_sha": "5c580db443878c702f9ec63c62c18951fe06ab0a",
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"installed_by": ["prepare_genome_dnaseq"]
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},
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"bwamem2/index": {
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"branch": "main",
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"git_sha": "4d329b41d14a20dec31cae811f39e1a52b435220",
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"git_sha": "5c580db443878c702f9ec63c62c18951fe06ab0a",
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"installed_by": ["prepare_genome_dnaseq"]
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},
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"dragmap/hashtable": {
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"branch": "main",
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"git_sha": "45771824ae473165222af14becffa213448a5edc",
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"git_sha": "5c580db443878c702f9ec63c62c18951fe06ab0a",
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"installed_by": ["prepare_genome_dnaseq"]
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},
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"gatk4/createsequencedictionary": {
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"branch": "main",
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"git_sha": "4d329b41d14a20dec31cae811f39e1a52b435220",
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"git_sha": "5c580db443878c702f9ec63c62c18951fe06ab0a",
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"installed_by": ["prepare_genome_dnaseq"]
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},
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"gawk": {
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"branch": "main",
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"git_sha": "4d329b41d14a20dec31cae811f39e1a52b435220",
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"git_sha": "5c580db443878c702f9ec63c62c18951fe06ab0a",
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"installed_by": ["prepare_genome_dnaseq"]
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},
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"gffread": {
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"branch": "main",
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"git_sha": "4d329b41d14a20dec31cae811f39e1a52b435220",
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"git_sha": "5c580db443878c702f9ec63c62c18951fe06ab0a",
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"installed_by": ["prepare_genome_rnaseq"]
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},
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"hisat2/build": {
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"branch": "main",
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"git_sha": "4d329b41d14a20dec31cae811f39e1a52b435220",
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"git_sha": "5c580db443878c702f9ec63c62c18951fe06ab0a",
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"installed_by": ["prepare_genome_rnaseq"]
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},
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"hisat2/extractsplicesites": {
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"branch": "main",
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"git_sha": "4d329b41d14a20dec31cae811f39e1a52b435220",
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"git_sha": "5c580db443878c702f9ec63c62c18951fe06ab0a",
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"installed_by": ["prepare_genome_rnaseq"]
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},
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"kallisto/index": {
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"branch": "main",
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"git_sha": "4d329b41d14a20dec31cae811f39e1a52b435220",
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"git_sha": "5c580db443878c702f9ec63c62c18951fe06ab0a",
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"installed_by": ["prepare_genome_rnaseq"]
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},
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"msisensorpro/scan": {
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"branch": "main",
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"git_sha": "8c1309daf37cd08ec9f98298521abd1f2745288a",
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"git_sha": "5c580db443878c702f9ec63c62c18951fe06ab0a",
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"installed_by": ["prepare_genome_dnaseq"]
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},
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"rsem/preparereference": {
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"branch": "main",
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"git_sha": "4d329b41d14a20dec31cae811f39e1a52b435220",
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"git_sha": "5c580db443878c702f9ec63c62c18951fe06ab0a",
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"installed_by": ["prepare_genome_rnaseq"]
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},
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"salmon/index": {
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"branch": "main",
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"git_sha": "4d329b41d14a20dec31cae811f39e1a52b435220",
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"git_sha": "5c580db443878c702f9ec63c62c18951fe06ab0a",
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"installed_by": ["prepare_genome_rnaseq"]
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},
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"samtools/faidx": {
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"branch": "main",
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"git_sha": "4d329b41d14a20dec31cae811f39e1a52b435220",
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"git_sha": "5c580db443878c702f9ec63c62c18951fe06ab0a",
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"installed_by": ["prepare_genome_dnaseq", "prepare_genome_rnaseq"]
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},
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"snapaligner/index": {
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"branch": "main",
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"git_sha": "5c580db443878c702f9ec63c62c18951fe06ab0a",
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"installed_by": ["prepare_genome_dnaseq"]
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},
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"star/genomegenerate": {
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"branch": "main",
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"git_sha": "4d329b41d14a20dec31cae811f39e1a52b435220",
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"git_sha": "5c580db443878c702f9ec63c62c18951fe06ab0a",
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"installed_by": ["prepare_genome_rnaseq"]
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},
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"tabix/bgziptabix": {
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"branch": "main",
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"git_sha": "4d329b41d14a20dec31cae811f39e1a52b435220",
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"git_sha": "5c580db443878c702f9ec63c62c18951fe06ab0a",
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"installed_by": ["prepare_genome_dnaseq"]
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},
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"tabix/tabix": {
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"branch": "main",
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"git_sha": "4d329b41d14a20dec31cae811f39e1a52b435220",
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"git_sha": "5c580db443878c702f9ec63c62c18951fe06ab0a",
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"installed_by": ["prepare_genome_dnaseq"]
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}
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}
@@ -166,17 +156,17 @@
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"nf-side": {
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"prepare_genome_dnaseq": {
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"branch": "main",
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"git_sha": "54a64244d279aeb3ad0ea1ebc2315db5878639cb",
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"git_sha": "3f81209f8ae9b11925da2a9a8bc57bfdb5028eef",
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"installed_by": ["subworkflows"]
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},
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"prepare_genome_rnaseq": {
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"branch": "main",
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"git_sha": "54a64244d279aeb3ad0ea1ebc2315db5878639cb",
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"git_sha": "3f81209f8ae9b11925da2a9a8bc57bfdb5028eef",
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"installed_by": ["subworkflows"]
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},
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"utils_references": {
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"branch": "main",
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"git_sha": "4ec95caec3353de5944ee72b5889906da3acc937",
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"git_sha": "3f81209f8ae9b11925da2a9a8bc57bfdb5028eef",
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"installed_by": ["subworkflows"]
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}
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}

‎modules/nf-core/bbmap/bbsplit/environment.yml‎

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‎modules/nf-core/bbmap/bbsplit/main.nf‎

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