nf-core · itrujnara · Jul 18, 2024 · Jun 11, 2024 · Jun 11, 2024 · Jun 11, 2024
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,6 +3,13 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [v1.0.1](https://github.com/nf-core/reportho/releases/tag/1.0.1) [2024-06-14]
+
+### `Fixed`
+
+- Fixed minor bugs that caused compilation errors in the structural alignment section
+- Restricted publishing of intermediate files
+
 ## [v1.0.0](https://github.com/nf-core/reportho/releases/tag/1.0.0) - Magnificent Mainsail - [2024-06-11]
 
 Although its location and design may vary greatly, the mainsail is always a key source of propulsion for a ship.

diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
@@ -1,7 +1,7 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/reportho/releases/tag/1.0.0" target="_blank">nf-core/reportho</a>
+  This report has been generated by the <a href="https://github.com/nf-core/reportho/releases/tag/1.0.1" target="_blank">nf-core/reportho</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/reportho/1.0.0/docs/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/reportho/1.0.1/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-reportho-methods-description":
     order: -1000

diff --git a/conf/modules.config b/conf/modules.config
@@ -79,6 +79,12 @@ process {
 
     withName: 'MERGE_CSV' {
         ext.args = '-f 1 --outer-join --na 0'
+        publishDir = [
+            path: { "${params.outdir}/orthologs/merge_csv" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+            enabled: params.output_intermediates
+        ]
     }
 
     withName: 'MAKE_SCORE_TABLE' {
@@ -106,6 +112,15 @@ process {
         ]
     }
 
+    withName: 'MAKE_HITS_TABLE' {
+        publishDir = [
+            path: { "${params.outdir}/orthologs/stats" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+            enabled: params.output_intermediates
+        ]
+    }
+
     withName: 'MERGE_HITS' {
         ext.args = "-u 0 -k"
         ext.prefix = "aggregated_hits"
@@ -116,6 +131,15 @@ process {
         ]
     }
 
+    withName: 'MAKE_STATS' {
+        publishDir = [
+            path: { "${params.outdir}/orthologs/stats" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+            enabled: params.output_intermediates
+        ]
+    }
+
     withName: 'MERGE_STATS' {
         ext.args = "-u NA"
         ext.prefix = "aggregated_stats"
@@ -159,6 +183,16 @@ process {
         ]
     }
 
+    withName: 'CREATE_TCOFFEETEMPLATE' {
+        publishDir = [
+            path: { "${params.outdir}/alignment/templates" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+            enabled: params.output_intermediates
+        ]
+
+    }
+
     withName: 'TCOFFEE_ALIGN|TCOFFEE_3DALIGN' {
         publishDir = [
             path: { "${params.outdir}/alignment/tcoffee" },
@@ -188,6 +222,15 @@ process {
         ]
     }
 
+    withName: 'CONVERT_PHYLIP' {
+        publishDir = [
+            path: { "${params.outdir}/trees/phylip" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+            enabled: params.output_intermediates
+        ]
+    }
+
     withName: 'FASTME' {
         ext.args = '-p LG' + (params.fastme_bootstrap > 0 ? ' -b ' + params.fastme_bootstrap : '')
         publishDir = [
@@ -218,6 +261,15 @@ process {
         ]
     }
 
+    withName: 'CONVERT_FASTA' {
+        publishDir = [
+            path: { "${params.outdir}/report/fasta" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+            enabled: params.output_intermediates
+        ]
+    }
+
     withName: 'MAKE_REPORT' {
         publishDir = [
             path: { "${params.outdir}/report" },

diff --git a/modules/local/fetch_afdb_structures.nf b/modules/local/fetch_afdb_structures.nf
@@ -26,7 +26,7 @@ process FETCH_AFDB_STRUCTURES {
     fetch_afdb_structures.py $ids $prefix 2> ${prefix}_af_versions.txt
 
     cat <<- END_VERSIONS > versions.yml
-    "${task.process}"
+    "${task.process}":
         Python: \$(python --version | cut -d ' ' -f 2)
         Python Requests: \$(pip show requests | grep Version | cut -d ' ' -f 2)
     END_VERSIONS
@@ -41,7 +41,7 @@ process FETCH_AFDB_STRUCTURES {
     touch ${prefix}_af_versions.txt
 
     cat <<- END_VERSIONS > versions.yml
-    "${task.process}"
+    "${task.process}":
         Python: \$(python --version | cut -d ' ' -f 2)
         Python Requests: \$(pip show requests | grep Version | cut -d ' ' -f 2)
     END_VERSIONS

diff --git a/nextflow.config b/nextflow.config
@@ -266,7 +266,7 @@ manifest {
     description     = """A pipeline for ortholog fetching and analysis"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
-    version         = '1.0.0'
+    version         = '1.0.1'
     doi             = '10.5281/zenodo.11574565'
 }
 

diff --git a/workflows/reportho.nf b/workflows/reportho.nf
@@ -95,7 +95,7 @@ workflow REPORTHO {
             ch_versions = ch_versions.mix(FETCH_AFDB_STRUCTURES.out.versions)
         }
 
-        ch_structures = params.use_structures ? FETCH_AFDB_STRUCTURES.out.structures : Channel.empty()
+        ch_structures = params.use_structures ? FETCH_AFDB_STRUCTURES.out.pdb : Channel.empty()
 
         ALIGN (
             FETCH_SEQUENCES_ONLINE.out.fasta,