nf-core · louperelo · Mar 20, 2023 · Mar 9, 2023 · Mar 9, 2023 · Mar 9, 2023
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -9,6 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Fixed`
 
+- [#243](https://github.com/nf-core/funcscan/pull/243) Compress the ampcombi_complete_summary.csv in the output directory (by @louperelo)
 - [#237](https://github.com/nf-core/funcscan/pull/237) Reactivate DeepARG automatic database downloading and CI tests as server is now back up. (by @jfy133)
 
 ### `Dependencies`

diff --git a/LICENSE b/LICENSE
@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) Jasmin Frangenberg, Anan Ibrahim, James A. Fellows Yates
+Copyright (c) Jasmin Frangenberg, Anan Ibrahim, Louisa Perelo, Moritz E. Beber, James A. Fellows Yates
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/conf/modules.config b/conf/modules.config
@@ -454,6 +454,14 @@ process {
         ext.args =  "--tooldict '${ext.tooldict}' --cutoff ${params.amp_ampcombi_cutoff}"
     }
 
+    withName: TABIX_BGZIP {
+        publishDir = [
+            path: { "${params.outdir}/reports/ampcombi" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
     withName: COMBGC {
         publishDir = [
             path: { "${params.outdir}/reports/combgc" },

diff --git a/docs/output.md b/docs/output.md
@@ -384,7 +384,7 @@ Output Summaries:
 <summary>Output files</summary>
 
 - `ampcombi/`
-  - `ampcombi_complete_summary.csv`: summarised output from all AMP workflow tools (except hmmer_hmmsearch) in csv format
+  - `ampcombi_complete_summary.csv.gz`: summarised output from all AMP workflow tools (except hmmer_hmmsearch) in compressed csv format
   - `ampcombi.log`: a log file generated by ampcombi
   - `*_ampcombi.csv`: summarised output in csv for each sample
   - `*_amp.faa*`: fasta file containing the amino acid sequences for all AMP hits for each sample

diff --git a/modules.json b/modules.json
@@ -166,6 +166,11 @@
                         "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
                         "installed_by": ["modules"]
                     },
+                    "tabix/bgzip": {
+                        "branch": "master",
+                        "git_sha": "90294980a903ecebd99ac31d8b6c66af48fa8259",
+                        "installed_by": ["modules"]
+                    },
                     "untar": {
                         "branch": "master",
                         "git_sha": "cc1f997fab6d8fde5dc0e6e2a310814df5b53ce7",

diff --git a/modules/nf-core/tabix/bgzip/main.nf b/modules/nf-core/tabix/bgzip/main.nf
diff --git a/modules/nf-core/tabix/bgzip/meta.yml b/modules/nf-core/tabix/bgzip/meta.yml
diff --git a/nextflow.config b/nextflow.config
@@ -339,7 +339,7 @@ dag {
 
 manifest {
     name            = 'nf-core/funcscan'
-    author          = """Jasmin Frangenberg, Anan Ibrahim, James A. Fellows Yates"""
+    author          = """Jasmin Frangenberg, Anan Ibrahim, Louisa Perelo, Moritz E. Beber, James A. Fellows Yates"""
     homePage        = 'https://github.com/nf-core/funcscan'
     description     = """Pipeline for screening for functional components of assembled contigs"""
     mainScript      = 'main.nf'

diff --git a/subworkflows/local/amp.nf b/subworkflows/local/amp.nf
@@ -8,6 +8,8 @@ include { AMPLIFY_PREDICT                                           } from '../.
 include { AMPIR                                                     } from '../../modules/nf-core/ampir/main'
 include { AMPCOMBI                                                  } from '../../modules/nf-core/ampcombi/main'
 include { GUNZIP as GUNZIP_MACREL ; GUNZIP as GUNZIP_HMMER          } from '../../modules/nf-core/gunzip/main'
+include { TABIX_BGZIP                                               } from '../../modules/nf-core/tabix/bgzip/main'
+
 
 workflow AMP {
     take:
@@ -96,7 +98,11 @@ workflow AMP {
                 input: [ it[0] ]
                 summary: it[1]
             }
-    ch_ampcombi_summaries_out.summary.collectFile(name: 'ampcombi_complete_summary.csv', storeDir: "${params.outdir}/reports/ampcombi", keepHeader:true)
+
+    ch_tabix_input = Channel.of(['id':'ampcombi_complete_summary'])
+        .combine(ch_ampcombi_summaries_out.summary.collectFile(name: 'ampcombi_complete_summary.csv', keepHeader:true))
+
+    TABIX_BGZIP(ch_tabix_input)
 
     emit:
     versions = ch_versions