From 24003720b6bb99a33f4ce21127db7dc8fbee09b9 Mon Sep 17 00:00:00 2001 From: Kyle O'Connell Date: Fri, 16 Feb 2024 15:17:30 -0500 Subject: [PATCH 01/10] moved bakta to call subworkflow --- .../local/{bakta_entry.nf => bakta.nf} | 41 ++++++++----------- workflows/tostadas.nf | 33 ++++----------- 2 files changed, 25 insertions(+), 49 deletions(-) rename subworkflows/local/{bakta_entry.nf => bakta.nf} (58%) diff --git a/subworkflows/local/bakta_entry.nf b/subworkflows/local/bakta.nf similarity index 58% rename from subworkflows/local/bakta_entry.nf rename to subworkflows/local/bakta.nf index d16f436b..ea67b370 100644 --- a/subworkflows/local/bakta_entry.nf +++ b/subworkflows/local/bakta.nf @@ -9,43 +9,34 @@ include { BAKTA } from "../../modules/nf-core/bakta/bakta/main" include { BAKTADBDOWNLOAD } from "../../modules/nf-core/bakta/baktadbdownload/main" include { BAKTA_POST_CLEANUP } from "../../modules/local/post_bakta_annotation/main" +// get BAKTA related processes workflow RUN_BAKTA { take: - run_utility - fasta + utility_signal + fasta_ch main: - if ( params.download_bakta_db ) { - BAKTADBDOWNLOAD ( - run_utility - ) - - BAKTA ( - run_utility, - BAKTADBDOWNLOAD.out.db, - fasta - ) + if ( params.download_bakta_db ) { + BAKTADBDOWNLOAD ( + utility_signal + ) + BAKTA ( + utility_signal, + BAKTADBDOWNLOAD.out.db, + fasta_ch + ) } - else { BAKTA ( - run_utility, - params.bakta_db_path, - fasta + utility_signal, + params.bakta_db_path, + fasta_ch ) } - BAKTA_POST_CLEANUP ( - BAKTA.out.bakta_results, - params.meta_path, - fasta - ) - emit: - cleaned_fasta = BAKTA_POST_CLEANUP.out.fasta - cleaned_gff = BAKTA_POST_CLEANUP.out.gff - + gff3 = BAKTA.out.gff3 } diff --git a/workflows/tostadas.nf b/workflows/tostadas.nf index 7aa866fb..2a943b66 100644 --- a/workflows/tostadas.nf +++ b/workflows/tostadas.nf @@ -16,13 +16,11 @@ include { METADATA_VALIDATION } from "../modules/l // get viral annotation process/subworkflows include { LIFTOFF } from "../modules/local/liftoff_annotation/main" -include { REPEATMASKER_LIFTOFF } from "../subworkflows/local/repeatmasker_liftoff" +include { REPEATMASKER_LIFTOFF } from "../subworkflows/local/repeatmasker_liftoff" include { RUN_VADR } from "../subworkflows/local/vadr" -// get BAKTA related processes -include { BAKTADBDOWNLOAD } from "../modules/nf-core/bakta/baktadbdownload/main" -include { BAKTA } from "../modules/nf-core/bakta/bakta/main" -include { BAKTA_POST_CLEANUP } from "../modules/local/post_bakta_annotation/main" +// get BAKTA subworkflow +include { RUN_BAKTA } from "../subworkflows/local/bakta" // get submission related process/subworkflows include { FULL_SUBMISSION } from "../subworkflows/local/full_submission" @@ -125,7 +123,7 @@ workflow TOSTADAS { if ( params.vadr ) { RUN_VADR ( RUN_UTILITY.out, - CHECK_FILES.out.fasta_files.sort().flatten() + fasta_ch ) vadr_gff_ch = RUN_VADR.out.collect().flatten() .map { @@ -138,30 +136,17 @@ workflow TOSTADAS { if ( params.bacteria ) { // run bakta annotation process if ( params.bakta == true ) { - if ( params.download_bakta_db ) { - BAKTADBDOWNLOAD ( - RUN_UTILITY.out + RUN_BAKTA( + RUN_UTILITY.out, + fasta_ch ) - BAKTA ( - RUN_UTILITY.out, - BAKTADBDOWNLOAD.out.db, - fasta_ch - ) - } - else { - BAKTA ( - RUN_UTILITY.out, - params.bakta_db_path, - fasta_ch - ) - bakta_gff_ch = BAKTA.out.gff3.flatten() + // set up submission channels + bakta_gff_ch = RUN_BAKTA.out.gff3.flatten() .map { def meta = [:] meta['id'] = it.getSimpleName() [ meta, it ] } - } - // set up submission channels submission_ch = metadata_ch.join(fasta_ch) submission_ch = submission_ch.join(bakta_gff_ch) } From a4b0afd5964791c7b3f9044c3257bde261bdc9c5 Mon Sep 17 00:00:00 2001 From: Kyle O'Connell Date: Fri, 16 Feb 2024 15:40:44 -0500 Subject: [PATCH 02/10] reformatted bakta --- conf/modules.config | 36 ++--------------------------- modules/nf-core/bakta/bakta/main.nf | 18 --------------- nextflow.config | 2 ++ 3 files changed, 4 insertions(+), 52 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index cb9fd74e..e1e600bb 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -17,37 +17,5 @@ process { mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] - - withName: BAKTA { - ext.args = { - [ - params.complete ? '--complete' : '', - params.meta ? '--meta' : '', - params.keep_contig_headers ? '--keep-contig-headers' : '', - params.version ? '--version' : '', - params.verbose ? '--verbose' : '', - params.help ? '--help' : '', - params.debug ? '--debug' : '', - params.skip_trna ? '--skip-trna' : '', - params.skip_tmrna ? '--skip-tmrna' : '', - params.skip_rrna ? '--skip-rrna' : '', - params.skip_ncrna ? '--skip-ncrna' : '', - params.skip_ncrna_region ? '--skip-ncrna-region' : '', - params.skip_crispr ? '--skip-crispr' : '', - params.skip_cds ? '--skip-cds' : '', - params.skip_pseudo ? '--skip-pseudo' : '', - params.skip_sorf ? '--skip-sorf' : '', - params.skip_gap ? '--skip-gap' : '', - params.skip_ori ? '--skip-ori' : '', - params.skip_plot ? '--skip-plot' : '', - params.bakta_min_contig_length ? '--min-contig-length', - params.bakta_genus ? '--genus', - params.bakta_species ? '--species', - params.bakta_strain ? '--strain', - params.bakta_plasmid ? '--plasmid', - params.bakta_locus ? '--locus', - params.bakta_locus_tag ? '--locus-tag', - params.bakta_translation_table ? '--translation-table' - ] - } - } \ No newline at end of file + +} \ No newline at end of file diff --git a/modules/nf-core/bakta/bakta/main.nf b/modules/nf-core/bakta/bakta/main.nf index 4c22b6b4..fd5a6ac9 100644 --- a/modules/nf-core/bakta/bakta/main.nf +++ b/modules/nf-core/bakta/bakta/main.nf @@ -40,24 +40,6 @@ process BAKTA { --keep-contig-headers \ $fasta_path """ - // optional args - // --prodigal-tf $params.bakta_prodigal_tf - // --replicons $params.bakta_replicons - // --proteins $params.bakta_proteins - // --skip-trna - // --skip-tmrna - // --skip-rrna - // --skip-ncrna - // --skip-ncrna-region - // --skip-crispr - // --skip-cds - // --skip-pseudo - // --skip-sorf - // --skip-gap - // --skip-ori - // --skip-plot - - output: path "${fasta_path.getSimpleName()}/*.fna", emit: fna diff --git a/nextflow.config b/nextflow.config index 65e72929..b3301a18 100644 --- a/nextflow.config +++ b/nextflow.config @@ -227,6 +227,8 @@ profiles { } } +// Load modules.config for DSL2 module specific options +includeConfig 'conf/modules.config' /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From 038eb0a0b391c92ab75c1fe8fa73eaf6c4f71ee3 Mon Sep 17 00:00:00 2001 From: Kyle O'Connell Date: Fri, 16 Feb 2024 15:59:21 -0500 Subject: [PATCH 03/10] added optional params for bakta --- conf/modules.config | 1 - modules/nf-core/bakta/bakta/main.nf | 30 +++++++++++++++++++++++++++-- nextflow.config | 1 + 3 files changed, 29 insertions(+), 3 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index e1e600bb..e47ff1c8 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -17,5 +17,4 @@ process { mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] - } \ No newline at end of file diff --git a/modules/nf-core/bakta/bakta/main.nf b/modules/nf-core/bakta/bakta/main.nf index fd5a6ac9..43df6196 100644 --- a/modules/nf-core/bakta/bakta/main.nf +++ b/modules/nf-core/bakta/bakta/main.nf @@ -21,6 +21,21 @@ process BAKTA { script: def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def proteins_opt = params.bakta_proteins ? "--proteins ${proteins[0]}" : "" + def prodigal_tf = params.bakta_prodigal_tf ? "--prodigal-tf ${prodigal_tf[0]}" : "" + def skip_trna = params.skip_trna ? "--skip_trna" : "" + def skip_tmrna = params.skip_tmrna ? "--skip_tmrna" : "" + def skip_rrna = params.skip_rrna ? "--skip_rrna" : "" + def skip_ncrna = params.skip_ncrna ? "--skip_ncrna" : "" + def skip_ncrna_region = params.skip_ncrna_region ? "--skip_ncrna_region" : "" + def skip_crispr = params.skip_crispr ? "--skip_crispr" : "" + def skip_cds = params.skip_cds ? "--skip_cds" : "" + def skip_sorf = params.skip_sorf ? "--skip_sorf" : "" + def skip_gap = params.skip_gap ? "--skip_gap" : "" + def skip_ori = params.skip_ori ? "--skip_ori" : "" + def compliant = params.compliant ? "--compliant" : "" + def keep_contig_headers = params.keep_contig_headers ? "--keep_contig_headers" : "" """ bakta --db $db_path \ @@ -34,10 +49,21 @@ process BAKTA { --complete $params.bakta_complete \ --translation-table $params.bakta_translation_table \ --gram $params.bakta_gram \ - --compliant \ --locus $params.bakta_locus \ --locus-tag $params.bakta_locus_tag \ - --keep-contig-headers \ + --$compliant \ + --$keep-contig-headers \ + --$proteins \ + --$prodigal-tf \ + --$skip_trna \ + --$skip_rrna \ + --$skip_ncrna \ + --$skip_ncrna_region \ + --$skip_crispr \ + --$skip_cds \ + --$skip_sorf \ + --$skip_gap \ + --$skip_ori \ $fasta_path """ diff --git a/nextflow.config b/nextflow.config index b3301a18..f8537af1 100644 --- a/nextflow.config +++ b/nextflow.config @@ -54,6 +54,7 @@ params { // general params help = false + publish_dir_mode = 'copy' output_dir = "" overwrite_output = false // To Do check if we need these three dirs From cd8ad1ce12479b1814366e69ab13812c8f69e59f Mon Sep 17 00:00:00 2001 From: Kyle O'Connell Date: Fri, 16 Feb 2024 16:06:50 -0500 Subject: [PATCH 04/10] added optional params for bakta --- modules/nf-core/bakta/bakta/main.nf | 24 ++++++++++++------------ nextflow.config | 9 +++++---- 2 files changed, 17 insertions(+), 16 deletions(-) diff --git a/modules/nf-core/bakta/bakta/main.nf b/modules/nf-core/bakta/bakta/main.nf index 43df6196..251a34fb 100644 --- a/modules/nf-core/bakta/bakta/main.nf +++ b/modules/nf-core/bakta/bakta/main.nf @@ -24,18 +24,18 @@ process BAKTA { def prefix = task.ext.prefix ?: "${meta.id}" def proteins_opt = params.bakta_proteins ? "--proteins ${proteins[0]}" : "" def prodigal_tf = params.bakta_prodigal_tf ? "--prodigal-tf ${prodigal_tf[0]}" : "" - def skip_trna = params.skip_trna ? "--skip_trna" : "" - def skip_tmrna = params.skip_tmrna ? "--skip_tmrna" : "" - def skip_rrna = params.skip_rrna ? "--skip_rrna" : "" - def skip_ncrna = params.skip_ncrna ? "--skip_ncrna" : "" - def skip_ncrna_region = params.skip_ncrna_region ? "--skip_ncrna_region" : "" - def skip_crispr = params.skip_crispr ? "--skip_crispr" : "" - def skip_cds = params.skip_cds ? "--skip_cds" : "" - def skip_sorf = params.skip_sorf ? "--skip_sorf" : "" - def skip_gap = params.skip_gap ? "--skip_gap" : "" - def skip_ori = params.skip_ori ? "--skip_ori" : "" - def compliant = params.compliant ? "--compliant" : "" - def keep_contig_headers = params.keep_contig_headers ? "--keep_contig_headers" : "" + def skip_trna = params.bakta_skip_trna ? "--skip_trna" : "" + def skip_tmrna = params.bakta_skip_tmrna ? "--skip_tmrna" : "" + def skip_rrna = params.bakta_skip_rrna ? "--skip_rrna" : "" + def skip_ncrna = params.bakta_skip_ncrna ? "--skip_ncrna" : "" + def skip_ncrna_region = params.bakta_skip_ncrna_region ? "--skip_ncrna_region" : "" + def skip_crispr = params.bakta_skip_crispr ? "--skip_crispr" : "" + def skip_cds = params.bakta_skip_cds ? "--skip_cds" : "" + def skip_sorf = params.bakta_skip_sorf ? "--skip_sorf" : "" + def skip_gap = params.bakta_skip_gap ? "--skip_gap" : "" + def skip_ori = params.bakta_skip_ori ? "--skip_ori" : "" + def compliant = params.bakta_compliant ? "--compliant" : "" + def keep_contig_headers = params.bakta_keep_contig_headers ? "--keep_contig_headers" : "" """ bakta --db $db_path \ diff --git a/nextflow.config b/nextflow.config index f8537af1..a5089f29 100644 --- a/nextflow.config +++ b/nextflow.config @@ -86,7 +86,7 @@ params { clear_nf_results = false overwrite_output = true - // batka annotation + // required bakta params bakta_output_dir = "" bakta_db_type = "light" // light or full download_bakta_db = false @@ -102,10 +102,11 @@ params { bakta_gram = "" bakta_locus = "contig" bakta_locus_tag = "LOCUSTAG123" // set a meaningful locus tag here for compliant mode - bakta_keep_contig_headers = "" - // optional bakta params, for now need to add these to modules/nf-core/bakta/bakta/main.nf - bakta_prodigal_df = "" + // optional bakta params + bakta_compliant = "" + bakta_keep_contig_headers = "" + bakta_prodigal_tf = "" bakta_replicons = "" bakta_proteins = "" bakta_skip_trna = "" From 6f78d5b18638607048546f9c0381899ef51c1b10 Mon Sep 17 00:00:00 2001 From: Kyle O'Connell Date: Fri, 16 Feb 2024 16:10:52 -0500 Subject: [PATCH 05/10] updated bakta params --- modules/nf-core/bakta/bakta/main.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/nf-core/bakta/bakta/main.nf b/modules/nf-core/bakta/bakta/main.nf index 251a34fb..a5d85450 100644 --- a/modules/nf-core/bakta/bakta/main.nf +++ b/modules/nf-core/bakta/bakta/main.nf @@ -52,9 +52,9 @@ process BAKTA { --locus $params.bakta_locus \ --locus-tag $params.bakta_locus_tag \ --$compliant \ - --$keep-contig-headers \ + --$keep_contig_headers \ --$proteins \ - --$prodigal-tf \ + --$prodigal_tf \ --$skip_trna \ --$skip_rrna \ --$skip_ncrna \ From 28da5d72781600b7eeeb9e49426df80eb560a6dc Mon Sep 17 00:00:00 2001 From: Kyle O'Connell Date: Fri, 16 Feb 2024 16:11:57 -0500 Subject: [PATCH 06/10] updated bakta params --- modules/nf-core/bakta/bakta/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/bakta/bakta/main.nf b/modules/nf-core/bakta/bakta/main.nf index a5d85450..a2e25736 100644 --- a/modules/nf-core/bakta/bakta/main.nf +++ b/modules/nf-core/bakta/bakta/main.nf @@ -22,7 +22,7 @@ process BAKTA { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def proteins_opt = params.bakta_proteins ? "--proteins ${proteins[0]}" : "" + def proteins = params.bakta_proteins ? "--proteins ${proteins[0]}" : "" def prodigal_tf = params.bakta_prodigal_tf ? "--prodigal-tf ${prodigal_tf[0]}" : "" def skip_trna = params.bakta_skip_trna ? "--skip_trna" : "" def skip_tmrna = params.bakta_skip_tmrna ? "--skip_tmrna" : "" From be3517c8c357564575798983950802215fcdbdb8 Mon Sep 17 00:00:00 2001 From: Kyle O'Connell Date: Fri, 16 Feb 2024 16:26:20 -0500 Subject: [PATCH 07/10] fixed the optional params by removing the -- from command --- modules/nf-core/bakta/bakta/main.nf | 27 ++++++++++++++------------- 1 file changed, 14 insertions(+), 13 deletions(-) diff --git a/modules/nf-core/bakta/bakta/main.nf b/modules/nf-core/bakta/bakta/main.nf index a2e25736..87352fa1 100644 --- a/modules/nf-core/bakta/bakta/main.nf +++ b/modules/nf-core/bakta/bakta/main.nf @@ -35,6 +35,7 @@ process BAKTA { def skip_gap = params.bakta_skip_gap ? "--skip_gap" : "" def skip_ori = params.bakta_skip_ori ? "--skip_ori" : "" def compliant = params.bakta_compliant ? "--compliant" : "" + def complete = params.bakta_complete ? "--complete" : "" def keep_contig_headers = params.bakta_keep_contig_headers ? "--keep_contig_headers" : "" """ @@ -51,19 +52,19 @@ process BAKTA { --gram $params.bakta_gram \ --locus $params.bakta_locus \ --locus-tag $params.bakta_locus_tag \ - --$compliant \ - --$keep_contig_headers \ - --$proteins \ - --$prodigal_tf \ - --$skip_trna \ - --$skip_rrna \ - --$skip_ncrna \ - --$skip_ncrna_region \ - --$skip_crispr \ - --$skip_cds \ - --$skip_sorf \ - --$skip_gap \ - --$skip_ori \ + $compliant \ + $keep_contig_headers \ + $proteins \ + $prodigal_tf \ + $skip_trna \ + $skip_rrna \ + $skip_ncrna \ + $skip_ncrna_region \ + $skip_crispr \ + $skip_cds \ + $skip_sorf \ + $skip_gap \ + $skip_ori \ $fasta_path """ From c2a9c07b6273b6a6cda6386341f88695bbd97321 Mon Sep 17 00:00:00 2001 From: Kyle O'Connell Date: Fri, 16 Feb 2024 16:36:59 -0500 Subject: [PATCH 08/10] fixed the optional params by removing the -- from command --- conf/test_params.config | 67 +++++++++++++++-------------- modules/nf-core/bakta/bakta/main.nf | 22 +++++----- 2 files changed, 45 insertions(+), 44 deletions(-) diff --git a/conf/test_params.config b/conf/test_params.config index 90cc5798..8e3793c1 100644 --- a/conf/test_params.config +++ b/conf/test_params.config @@ -140,39 +140,40 @@ params { BAKTA ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ - bakta_output_dir = "bakta_outputs" - bakta_db_type = "light" // light or full - download_bakta_db = false - bakta_db_path = "" - bakta_min_contig_length = 200 // due to compliant mode default, otherwise default is 1 - bakta_genus = "Genus" - bakta_species = "species" - bakta_strain = "strain" - bakta_plasmid = "unnamed" - bakta_complete = "" - bakta_compliant = "" - bakta_translation_table = 11 - bakta_gram = "?" - bakta_locus = "contig" - bakta_locus_tag = "LOCUSTAG123" // set a meaningful locus tag here for compliant mode - bakta_keep_contig_headers = "" - // optional bakta params, for now need to add these to modules/nf-core/bakta/bakta/main.nf - bakta_prodigal_df = "" - bakta_replicons = "" - bakta_proteins = "" - bakta_skip_trna = "" - bakta_skip_tmrna = "" - bakta_skip_rrna = "" - bakta_skip_ncrna = "" - bakta_skip_ncrna_region = "" - bakta_skip_crispr = "" - bakta_skip_cds = "" - bakta_skip_pseudo = "" - bakta_skip_sorf = "" - bakta_skip_gap = "" - bakta_skip_ori = "" - bakta_skip_plot = "" - + // required bakta params + bakta_output_dir = "" + bakta_db_type = "light" // light or full + download_bakta_db = false + bakta_db_path = "" + bakta_min_contig_length = 200 // due to compliant mode default, otherwise default is 1 + bakta_genus = "" + bakta_species = "" + bakta_strain = "" + bakta_plasmid = "unnamed" + bakta_complete = "" + bakta_compliant = true + bakta_translation_table = 11 + bakta_gram = "" + bakta_locus = "contig" + bakta_locus_tag = "LOCUSTAG123" // set a meaningful locus tag here for compliant mode + + // optional bakta params + bakta_keep_contig_headers = "" + bakta_prodigal_tf = "" + bakta_replicons = "" + bakta_proteins = "" + bakta_skip_trna = "" + bakta_skip_tmrna = "" + bakta_skip_rrna = "" + bakta_skip_ncrna = "" + bakta_skip_ncrna_region = "" + bakta_skip_crispr = "" + bakta_skip_cds = "" + bakta_skip_pseudo = "" + bakta_skip_sorf = "" + bakta_skip_gap = "" + bakta_skip_ori = "" + bakta_skip_plot = "" /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SUBMISSION diff --git a/modules/nf-core/bakta/bakta/main.nf b/modules/nf-core/bakta/bakta/main.nf index 87352fa1..e65418f8 100644 --- a/modules/nf-core/bakta/bakta/main.nf +++ b/modules/nf-core/bakta/bakta/main.nf @@ -24,19 +24,19 @@ process BAKTA { def prefix = task.ext.prefix ?: "${meta.id}" def proteins = params.bakta_proteins ? "--proteins ${proteins[0]}" : "" def prodigal_tf = params.bakta_prodigal_tf ? "--prodigal-tf ${prodigal_tf[0]}" : "" - def skip_trna = params.bakta_skip_trna ? "--skip_trna" : "" - def skip_tmrna = params.bakta_skip_tmrna ? "--skip_tmrna" : "" - def skip_rrna = params.bakta_skip_rrna ? "--skip_rrna" : "" - def skip_ncrna = params.bakta_skip_ncrna ? "--skip_ncrna" : "" - def skip_ncrna_region = params.bakta_skip_ncrna_region ? "--skip_ncrna_region" : "" - def skip_crispr = params.bakta_skip_crispr ? "--skip_crispr" : "" - def skip_cds = params.bakta_skip_cds ? "--skip_cds" : "" - def skip_sorf = params.bakta_skip_sorf ? "--skip_sorf" : "" - def skip_gap = params.bakta_skip_gap ? "--skip_gap" : "" - def skip_ori = params.bakta_skip_ori ? "--skip_ori" : "" + def skip_trna = params.bakta_skip_trna ? "--skip-trna" : "" + def skip_tmrna = params.bakta_skip_tmrna ? "--skip-tmrna" : "" + def skip_rrna = params.bakta_skip_rrna ? "--skip-rrna" : "" + def skip_ncrna = params.bakta_skip_ncrna ? "--skip-ncrna" : "" + def skip_ncrna_region = params.bakta_skip_ncrna_region ? "--skip-ncrna-region" : "" + def skip_crispr = params.bakta_skip_crispr ? "--skip-crispr" : "" + def skip_cds = params.bakta_skip_cds ? "--skip-cds" : "" + def skip_sorf = params.bakta_skip_sorf ? "--skip-sorf" : "" + def skip_gap = params.bakta_skip_gap ? "--skip-gap" : "" + def skip_ori = params.bakta_skip_ori ? "--skip-ori" : "" def compliant = params.bakta_compliant ? "--compliant" : "" def complete = params.bakta_complete ? "--complete" : "" - def keep_contig_headers = params.bakta_keep_contig_headers ? "--keep_contig_headers" : "" + def keep_contig_headers = params.bakta_keep_contig_headers ? "--keep-contig-headers" : "" """ bakta --db $db_path \ From 9161597ba5d0b3804d5718a4efcbe7efee27bbbd Mon Sep 17 00:00:00 2001 From: Kyle O'Connell Date: Mon, 19 Feb 2024 09:46:34 -0500 Subject: [PATCH 09/10] updated bakta outputdir --- conf/test_params.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/test_params.config b/conf/test_params.config index 8e3793c1..ddca8179 100644 --- a/conf/test_params.config +++ b/conf/test_params.config @@ -141,7 +141,7 @@ params { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ // required bakta params - bakta_output_dir = "" + bakta_output_dir = "bakta_outputs" bakta_db_type = "light" // light or full download_bakta_db = false bakta_db_path = "" From 85c3e124b4bf245f6f433b933b62910d8772c66c Mon Sep 17 00:00:00 2001 From: Kyle O'Connell Date: Mon, 19 Feb 2024 09:49:38 -0500 Subject: [PATCH 10/10] updated bakta outputdir --- conf/test_params.config | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/conf/test_params.config b/conf/test_params.config index ddca8179..952d44f3 100644 --- a/conf/test_params.config +++ b/conf/test_params.config @@ -146,14 +146,14 @@ params { download_bakta_db = false bakta_db_path = "" bakta_min_contig_length = 200 // due to compliant mode default, otherwise default is 1 - bakta_genus = "" - bakta_species = "" - bakta_strain = "" + bakta_genus = "Genus" + bakta_species = "species" + bakta_strain = "unnamed" bakta_plasmid = "unnamed" bakta_complete = "" bakta_compliant = true bakta_translation_table = 11 - bakta_gram = "" + bakta_gram = "?" bakta_locus = "contig" bakta_locus_tag = "LOCUSTAG123" // set a meaningful locus tag here for compliant mode