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Fix comments fro @maxulysse 
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5 files changed

+49
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lines changed

‎subworkflows/local/amp.nf‎

Lines changed: 7 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -2,17 +2,17 @@
22
Run AMP screening tools
33
*/
44

5-
include { MACREL_CONTIGS } from '../../modules/nf-core/macrel/contigs/main'
6-
include { HMMER_HMMSEARCH as AMP_HMMER_HMMSEARCH } from '../../modules/nf-core/hmmer/hmmsearch/main'
7-
include { AMPLIFY_PREDICT } from '../../modules/nf-core/amplify/predict/main'
8-
include { AMPIR } from '../../modules/nf-core/ampir/main'
5+
include { MACREL_CONTIGS } from '../../modules/nf-core/macrel/contigs'
6+
include { HMMER_HMMSEARCH as AMP_HMMER_HMMSEARCH } from '../../modules/nf-core/hmmer/hmmsearch'
7+
include { AMPLIFY_PREDICT } from '../../modules/nf-core/amplify/predict'
8+
include { AMPIR } from '../../modules/nf-core/ampir'
99
include { AMP_DATABASE_DOWNLOAD } from '../../modules/local/amp_database_download'
1010
include { AMPCOMBI2_PARSETABLES } from '../../modules/nf-core/ampcombi2/parsetables'
1111
include { AMPCOMBI2_COMPLETE } from '../../modules/nf-core/ampcombi2/complete'
1212
include { AMPCOMBI2_CLUSTER } from '../../modules/nf-core/ampcombi2/cluster'
13-
include { GUNZIP as GUNZIP_MACREL_PRED ; GUNZIP as GUNZIP_MACREL_ORFS } from '../../modules/nf-core/gunzip/main'
14-
include { GUNZIP as AMP_GUNZIP_HMMER_HMMSEARCH } from '../../modules/nf-core/gunzip/main'
15-
include { TABIX_BGZIP as AMP_TABIX_BGZIP } from '../../modules/nf-core/tabix/bgzip/main'
13+
include { GUNZIP as GUNZIP_MACREL_PRED ; GUNZIP as GUNZIP_MACREL_ORFS } from '../../modules/nf-core/gunzip'
14+
include { GUNZIP as AMP_GUNZIP_HMMER_HMMSEARCH } from '../../modules/nf-core/gunzip'
15+
include { TABIX_BGZIP as AMP_TABIX_BGZIP } from '../../modules/nf-core/tabix/bgzip'
1616
include { MERGE_TAXONOMY_AMPCOMBI } from '../../modules/local/merge_taxonomy_ampcombi'
1717

1818
workflow AMP {

‎subworkflows/local/annotation.nf‎

Lines changed: 11 additions & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -2,17 +2,17 @@
22
Run annotation tools
33
*/
44

5-
include { PROKKA } from '../../modules/nf-core/prokka/main'
6-
include { PRODIGAL } from '../../modules/nf-core/prodigal/main'
7-
include { PYRODIGAL } from '../../modules/nf-core/pyrodigal/main'
8-
include { BAKTA_BAKTADBDOWNLOAD } from '../../modules/nf-core/bakta/baktadbdownload/main'
9-
include { BAKTA_BAKTA } from '../../modules/nf-core/bakta/bakta/main'
10-
include { GUNZIP as GUNZIP_PRODIGAL_FNA } from '../../modules/nf-core/gunzip/main'
11-
include { GUNZIP as GUNZIP_PRODIGAL_FAA } from '../../modules/nf-core/gunzip/main'
12-
include { GUNZIP as GUNZIP_PRODIGAL_GBK } from '../../modules/nf-core/gunzip/main'
13-
include { GUNZIP as GUNZIP_PYRODIGAL_FNA } from '../../modules/nf-core/gunzip/main'
14-
include { GUNZIP as GUNZIP_PYRODIGAL_FAA } from '../../modules/nf-core/gunzip/main'
15-
include { GUNZIP as GUNZIP_PYRODIGAL_GBK } from '../../modules/nf-core/gunzip/main'
5+
include { PROKKA } from '../../modules/nf-core/prokka'
6+
include { PRODIGAL } from '../../modules/nf-core/prodigal'
7+
include { PYRODIGAL } from '../../modules/nf-core/pyrodigal'
8+
include { BAKTA_BAKTADBDOWNLOAD } from '../../modules/nf-core/bakta/baktadbdownload'
9+
include { BAKTA_BAKTA } from '../../modules/nf-core/bakta/bakta'
10+
include { GUNZIP as GUNZIP_PRODIGAL_FNA } from '../../modules/nf-core/gunzip'
11+
include { GUNZIP as GUNZIP_PRODIGAL_FAA } from '../../modules/nf-core/gunzip'
12+
include { GUNZIP as GUNZIP_PRODIGAL_GBK } from '../../modules/nf-core/gunzip'
13+
include { GUNZIP as GUNZIP_PYRODIGAL_FNA } from '../../modules/nf-core/gunzip'
14+
include { GUNZIP as GUNZIP_PYRODIGAL_FAA } from '../../modules/nf-core/gunzip'
15+
include { GUNZIP as GUNZIP_PYRODIGAL_GBK } from '../../modules/nf-core/gunzip'
1616

1717
workflow ANNOTATION {
1818
take:

‎subworkflows/local/arg.nf‎

Lines changed: 19 additions & 19 deletions
Original file line numberDiff line numberDiff line change
@@ -2,26 +2,26 @@
22
Run ARG screening tools
33
*/
44

5-
include { ABRICATE_RUN } from '../../modules/nf-core/abricate/run/main'
6-
include { AMRFINDERPLUS_UPDATE } from '../../modules/nf-core/amrfinderplus/update/main'
7-
include { AMRFINDERPLUS_RUN } from '../../modules/nf-core/amrfinderplus/run/main'
8-
include { DEEPARG_DOWNLOADDATA } from '../../modules/nf-core/deeparg/downloaddata/main'
9-
include { DEEPARG_PREDICT } from '../../modules/nf-core/deeparg/predict/main'
10-
include { FARGENE } from '../../modules/nf-core/fargene/main'
11-
include { RGI_CARDANNOTATION } from '../../modules/nf-core/rgi/cardannotation/main'
12-
include { RGI_MAIN } from '../../modules/nf-core/rgi/main/main'
13-
include { UNTAR as UNTAR_CARD } from '../../modules/nf-core/untar/main'
14-
include { TABIX_BGZIP as ARG_TABIX_BGZIP } from '../../modules/nf-core/tabix/bgzip/main'
5+
include { ABRICATE_RUN } from '../../modules/nf-core/abricate/run'
6+
include { AMRFINDERPLUS_UPDATE } from '../../modules/nf-core/amrfinderplus/update'
7+
include { AMRFINDERPLUS_RUN } from '../../modules/nf-core/amrfinderplus/run'
8+
include { DEEPARG_DOWNLOADDATA } from '../../modules/nf-core/deeparg/downloaddata'
9+
include { DEEPARG_PREDICT } from '../../modules/nf-core/deeparg/predict'
10+
include { FARGENE } from '../../modules/nf-core/fargene'
11+
include { RGI_CARDANNOTATION } from '../../modules/nf-core/rgi/cardannotation'
12+
include { RGI_MAIN } from '../../modules/nf-core/rgi/main'
13+
include { UNTAR as UNTAR_CARD } from '../../modules/nf-core/untar'
14+
include { TABIX_BGZIP as ARG_TABIX_BGZIP } from '../../modules/nf-core/tabix/bgzip'
1515
include { MERGE_TAXONOMY_HAMRONIZATION } from '../../modules/local/merge_taxonomy_hamronization'
16-
include { HAMRONIZATION_RGI } from '../../modules/nf-core/hamronization/rgi/main'
17-
include { HAMRONIZATION_FARGENE } from '../../modules/nf-core/hamronization/fargene/main'
18-
include { HAMRONIZATION_SUMMARIZE } from '../../modules/nf-core/hamronization/summarize/main'
19-
include { HAMRONIZATION_ABRICATE } from '../../modules/nf-core/hamronization/abricate/main'
20-
include { HAMRONIZATION_DEEPARG } from '../../modules/nf-core/hamronization/deeparg/main'
21-
include { HAMRONIZATION_AMRFINDERPLUS } from '../../modules/nf-core/hamronization/amrfinderplus/main'
22-
include { ARGNORM as ARGNORM_DEEPARG } from '../../modules/nf-core/argnorm/main'
23-
include { ARGNORM as ARGNORM_ABRICATE } from '../../modules/nf-core/argnorm/main'
24-
include { ARGNORM as ARGNORM_AMRFINDERPLUS } from '../../modules/nf-core/argnorm/main'
16+
include { HAMRONIZATION_RGI } from '../../modules/nf-core/hamronization/rgi'
17+
include { HAMRONIZATION_FARGENE } from '../../modules/nf-core/hamronization/fargene'
18+
include { HAMRONIZATION_SUMMARIZE } from '../../modules/nf-core/hamronization/summarize'
19+
include { HAMRONIZATION_ABRICATE } from '../../modules/nf-core/hamronization/abricate'
20+
include { HAMRONIZATION_DEEPARG } from '../../modules/nf-core/hamronization/deeparg'
21+
include { HAMRONIZATION_AMRFINDERPLUS } from '../../modules/nf-core/hamronization/amrfinderplus'
22+
include { ARGNORM as ARGNORM_DEEPARG } from '../../modules/nf-core/argnorm'
23+
include { ARGNORM as ARGNORM_ABRICATE } from '../../modules/nf-core/argnorm'
24+
include { ARGNORM as ARGNORM_AMRFINDERPLUS } from '../../modules/nf-core/argnorm'
2525

2626
workflow ARG {
2727
take:

‎subworkflows/local/bgc.nf‎

Lines changed: 9 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -2,17 +2,17 @@
22
Run BGC screening tools
33
*/
44

5-
include { UNTAR as UNTAR_ANTISMASHDB } from '../../modules/nf-core/untar/main'
6-
include { ANTISMASH_ANTISMASHDOWNLOADDATABASES } from '../../modules/nf-core/antismash/antismashdownloaddatabases/main'
7-
include { ANTISMASH_ANTISMASH } from '../../modules/nf-core/antismash/antismash/main'
8-
include { GECCO_RUN } from '../../modules/nf-core/gecco/run/main'
9-
include { HMMER_HMMSEARCH as BGC_HMMER_HMMSEARCH } from '../../modules/nf-core/hmmer/hmmsearch/main'
10-
include { DEEPBGC_DOWNLOAD } from '../../modules/nf-core/deepbgc/download/main'
11-
include { DEEPBGC_PIPELINE } from '../../modules/nf-core/deepbgc/pipeline/main'
5+
include { UNTAR as UNTAR_ANTISMASHDB } from '../../modules/nf-core/untar'
6+
include { ANTISMASH_ANTISMASHDOWNLOADDATABASES } from '../../modules/nf-core/antismash/antismashdownloaddatabases'
7+
include { ANTISMASH_ANTISMASH } from '../../modules/nf-core/antismash/antismash'
8+
include { GECCO_RUN } from '../../modules/nf-core/gecco/run'
9+
include { HMMER_HMMSEARCH as BGC_HMMER_HMMSEARCH } from '../../modules/nf-core/hmmer/hmmsearch'
10+
include { DEEPBGC_DOWNLOAD } from '../../modules/nf-core/deepbgc/download'
11+
include { DEEPBGC_PIPELINE } from '../../modules/nf-core/deepbgc/pipeline'
1212
include { COMBGC } from '../../modules/local/combgc'
13-
include { TABIX_BGZIP as BGC_TABIX_BGZIP } from '../../modules/nf-core/tabix/bgzip/main'
13+
include { TABIX_BGZIP as BGC_TABIX_BGZIP } from '../../modules/nf-core/tabix/bgzip'
1414
include { MERGE_TAXONOMY_COMBGC } from '../../modules/local/merge_taxonomy_combgc'
15-
include { GECCO_CONVERT } from '../../modules/nf-core/gecco/convert/main'
15+
include { GECCO_CONVERT } from '../../modules/nf-core/gecco/convert'
1616

1717
workflow BGC {
1818
take:

‎workflows/funcscan.nf‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -35,9 +35,9 @@ include { TAXA_CLASS } from '../subworkflows/local/taxa_cla
3535
//
3636
// MODULE: Installed directly from nf-core/modules
3737
//
38-
include { GUNZIP as GUNZIP_INPUT_PREP } from '../modules/nf-core/gunzip/main'
39-
include { SEQKIT_SEQ as SEQKIT_SEQ_LENGTH } from '../modules/nf-core/seqkit/seq/main'
40-
include { SEQKIT_SEQ as SEQKIT_SEQ_FILTER } from '../modules/nf-core/seqkit/seq/main'
38+
include { GUNZIP as GUNZIP_INPUT_PREP } from '../modules/nf-core/gunzip'
39+
include { SEQKIT_SEQ as SEQKIT_SEQ_LENGTH } from '../modules/nf-core/seqkit/seq'
40+
include { SEQKIT_SEQ as SEQKIT_SEQ_FILTER } from '../modules/nf-core/seqkit/seq'
4141

4242
/*
4343
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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