Update docs + database params, skip hmmsearch

CHANGELOG.md

@@ -28,6 +28,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#371](https://github.com/nf-core/funcscan/pull/371) Fixed AMRFinderPlus parameter `arg_amrfinderplus_name`. (by @m3hdad)
 - [#376](https://github.com/nf-core/funcscan/pull/376) Fixed an occasional RGI process failure when certain files not produced. (❤️ to @amizeranschi for reporting, fix by @amizeranschi & @jfy133)
 - [#386](https://github.com/nf-core/funcscan/pull/386) Updated DeepBGC module to fix output file names, separate annotation step for all BGC tools, add warning if no BGCs found, fix MultiQC reporting of annotation workflow. (by @jfy133, @jasmezz)
+- [#391](https://github.com/nf-core/funcscan/pull/391) Skip hmmmsearch by default to not crash pipeline if user provides no HMM files, updated all "database" parameters, updated docs. (by @jasmezz)
 
 ### `Dependencies`
 

conf/modules.config

@@ -37,19 +37,19 @@ process {
         publishDir = [
             path: { "${params.outdir}/databases/mmseqs/" },
             mode: params.publish_dir_mode,
-            enabled: params.save_databases,
+            enabled: params.save_db,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
         ext.args = [
-            params.taxa_classification_mmseqs_databases_savetmp ? "" : "--remove-tmp-files" ,
+            params.taxa_classification_mmseqs_db_savetmp ? "" : "--remove-tmp-files" ,
         ].join(' ').trim()
     }
 
     withName: MMSEQS_CREATEDB {
         publishDir = [
             path: { "${params.outdir}/databases/mmseqs/mmseqs_createdb/" },
             mode: params.publish_dir_mode,
-            enabled: params.save_databases,
+            enabled: params.save_db,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
@@ -58,7 +58,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/databases/mmseqs/mmseqs_taxonomy/" },
             mode: params.publish_dir_mode,
-            enabled: params.save_databases,
+            enabled: params.save_db,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
         ext.args = [
@@ -124,7 +124,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/databases/bakta" },
             mode: params.publish_dir_mode,
-            enabled: params.save_databases,
+            enabled: params.save_db,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
         ext.args = [
@@ -203,7 +203,7 @@ process {
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
         ext.args =  [
-            "--db ${params.arg_abricate_db}",
+            "--db ${params.arg_abricate_db_id}",
             "--minid ${params.arg_abricate_minid}",
             "--mincov ${params.arg_abricate_mincov}"
         ].join(' ').trim()
@@ -213,7 +213,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/databases/amrfinderplus" },
             mode: params.publish_dir_mode,
-            enabled: params.save_databases,
+            enabled: params.save_db,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
@@ -239,7 +239,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/databases/deeparg" },
             mode: params.publish_dir_mode,
-            enabled: params.save_databases,
+            enabled: params.save_db,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
@@ -301,7 +301,7 @@ process {
             [
                 path: { "${params.outdir}/databases/rgi" },
                 mode: params.publish_dir_mode,
-                enabled: params.save_databases,
+                enabled: params.save_db,
                 saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
             ]
         ]
@@ -313,7 +313,7 @@ process {
             [
                 path: { "${params.outdir}/databases/rgi" },
                 mode: params.publish_dir_mode,
-                enabled: params.save_databases,
+                enabled: params.save_db,
                 saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
             ]
         ]
@@ -423,7 +423,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/databases/antismash" },
             mode: params.publish_dir_mode,
-            enabled: params.save_databases,
+            enabled: params.save_db,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
@@ -432,7 +432,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/databases/deepbgc" },
             mode: params.publish_dir_mode,
-            enabled: params.save_databases,
+            enabled: params.save_db,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
@@ -646,7 +646,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/databases/dramp" },
             mode: params.publish_dir_mode,
-            enabled: params.save_databases,
+            enabled: params.save_db,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }

docs/output.md

@@ -8,9 +8,9 @@ The output of nf-core/funcscan provides reports for each of the functional group
 - antimicrobial peptides (tools: [Macrel](https://github.com/BigDataBiology/macrel), [AMPlify](https://github.com/bcgsc/AMPlify), [ampir](https://ampir.marine-omics.net), [hmmsearch](http://hmmer.org) – summarised by [AMPcombi](https://github.com/Darcy220606/AMPcombi))
 - biosynthetic gene clusters (tools: [antiSMASH](https://docs.antismash.secondarymetabolites.org), [DeepBGC](https://github.com/Merck/deepbgc), [GECCO](https://gecco.embl.de), [hmmsearch](http://hmmer.org) – summarised by [comBGC](#combgc))
 
-As a general workflow, we recommend to first look at the summary reports ([ARGs](#hamronization), [AMPs](#ampcombi), [BGCs](#combgc)), to get a general overview of what hits have been found across all the tools of each functional group. After which, you can explore the specific output directories of each tool to get more detailed information about each result. The tool-specific output directories also includes the output from the functional annotation steps of either [prokka](https://github.com/tseemann/prokka), [pyrodigal](https://github.com/althonos/pyrodigal), [prodigal](https://github.com/hyattpd/Prodigal), or [Bakta](https://github.com/oschwengers/bakta) if the `--save_annotations` flag was set. Additionally, taxonomic classifications from [MMseqs2](https://github.com/soedinglab/MMseqs2) are saved if the `--taxa_classification_mmseqs_databases_savetmp` and `--taxa_classification_mmseqs_taxonomy_savetmp` flags are set.
+As a general workflow, we recommend to first look at the summary reports ([ARGs](#hamronization), [AMPs](#ampcombi), [BGCs](#combgc)), to get a general overview of what hits have been found across all the tools of each functional group. After which, you can explore the specific output directories of each tool to get more detailed information about each result. The tool-specific output directories also includes the output from the functional annotation steps of either [prokka](https://github.com/tseemann/prokka), [pyrodigal](https://github.com/althonos/pyrodigal), [prodigal](https://github.com/hyattpd/Prodigal), or [Bakta](https://github.com/oschwengers/bakta) if the `--save_annotations` flag was set. Additionally, taxonomic classifications from [MMseqs2](https://github.com/soedinglab/MMseqs2) are saved if the `--taxa_classification_mmseqs_db_savetmp` and `--taxa_classification_mmseqs_taxonomy_savetmp` flags are set.
 
-Similarly, all downloaded databases are saved (i.e. from [MMseqs2](https://github.com/soedinglab/MMseqs2), [antiSMASH](https://docs.antismash.secondarymetabolites.org), [AMRFinderPlus](https://www.ncbi.nlm.nih.gov/pathogens/antimicrobial-resistance/AMRFinder), [Bakta](https://github.com/oschwengers/bakta), [DeepARG](https://bitbucket.org/gusphdproj/deeparg-ss/src/master), [RGI](https://github.com/arpcard/rgi), and/or [AMPcombi](https://github.com/Darcy220606/AMPcombi)) into the output directory `<outdir>/databases/` if the `--save_databases` flag was set.
+Similarly, all downloaded databases are saved (i.e. from [MMseqs2](https://github.com/soedinglab/MMseqs2), [antiSMASH](https://docs.antismash.secondarymetabolites.org), [AMRFinderPlus](https://www.ncbi.nlm.nih.gov/pathogens/antimicrobial-resistance/AMRFinder), [Bakta](https://github.com/oschwengers/bakta), [DeepARG](https://bitbucket.org/gusphdproj/deeparg-ss/src/master), [RGI](https://github.com/arpcard/rgi), and/or [AMPcombi](https://github.com/Darcy220606/AMPcombi)) into the output directory `<outdir>/databases/` if the `--save_db` flag was set.
 
 Furthermore, for reproducibility, versions of all software used in the run is presented in a [MultiQC](http://multiqc.info) report.