Merge pull request #18 from itrujnara/bug_fixes

Bug fixes

CHANGELOG.md

@@ -5,12 +5,62 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## v1.0dev - [date]
 
-Initial release of nf-core/reportho, created with the [nf-core](https://nf-co.re/) template.
+Although its location and design may vary greatly, the mainsail is always a key source of propulsion for a ship.
+
+This is the initial release of nf-core/reportho, created with the [nf-core](https://nf-co.re/) template.
+
+### `Credits`
+
+The following people have made significant contributions to the release through design, development and review:
+
+- [Igor Trujnara](https://github.com/itrujnara)
+- [Luisa Santus](https://github.com/luisas)
+- [Jose Espinosa-Carrasco](https://github.com/JoseEspinosa)
+- [Alessio Vignoli](https://github.com/alessiovignoli)
+
+We also thank everyone else from the nf-core community who has participated in planning and development.
 
 ### `Added`
 
+The pipeline was created. In particular, it has the following features:
+
+- fetching of ortholog predictions from public databases, through APIs and from local snapshots
+- systematic comparison of the predictions and calculation of comparison statistics
+- creation of an ortholog list with user-defined criteria
+- basic downstream analysis of the obtained ortholog list
+- generation of a human-readable report
+
 ### `Fixed`
 
+Nothing yet.
+
 ### `Dependencies`
 
+The pipeline has the following notable dependencies:
+
+| Program         | Version |
+| --------------- | ------- |
+| Python          | 3.11.0  |
+| Python Requests | 2.31.0  |
+| Biopython       | 1.83    |
+| R               | 4.3.3   |
+| PyYAML          | 5.4.1   |
+| T-COFFEE        | 13.46.0 |
+| pigz            | 2.8     |
+| csvtk           | 0.26.0  |
+| Node            | 21.6.2  |
+| Yarn            | 1.22.19 |
+| React           | 18.3.1  |
+
+At release date, the following database versions were current and used for testing the pipeline:
+
+| Database       | Version       |
+| -------------- | ------------- |
+| OMA            | Jul2023       |
+| PANTHER        | 18            |
+| OrthoInspector | Eukaryota2023 |
+| EggNOG         | 5.0           |
+
 ### `Deprecated`
+
+Nothing.

README.md

@@ -18,9 +18,6 @@
 
 ## Introduction
 
-> [!WARNING]
-> This pipeline is still in active development. While the overall design will remain stable, all technical details, such as parameter names, are subject to change without notice.
-
 **nf-core/reportho** is a bioinformatics pipeline that compares and assembles orthology predictions for a query protein. It fetches ortholog lists for a query (or its closest annotated homolog) from public sources, calculates pairwise and global agreement, and generates a consensus list with the desired level of confidence. Optionally, it offers common analysis on the consensus orthologs, such as MSA and phylogeny reconstruction. Additionally, it generates a clean, human-readable report of the results.
 
 <!-- Tube map -->

bin/fetch_oma_by_sequence.py

@@ -35,7 +35,7 @@ def main() -> None:
                 break
 
     # Write exact match status
-    if entry["identified_by"] == "exact match":
+    if json["identified_by"] == "exact match":
         print("true", file=open(sys.argv[4], 'w'))
     else:
         print("false", file=open(sys.argv[4], 'w'))

modules.json

@@ -51,7 +51,7 @@
                 "nf-core": {
                     "utils_nextflow_pipeline": {
                         "branch": "master",
-                        "git_sha": "cd08c91373cd00a73255081340e4914485846ba1",
+                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfcore_pipeline": {
@@ -61,7 +61,7 @@
                     },
                     "utils_nfvalidation_plugin": {
                         "branch": "master",
-                        "git_sha": "cd08c91373cd00a73255081340e4914485846ba1",
+                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
                         "installed_by": ["subworkflows"]
                     }
                 }

modules/local/dump_params.nf

@@ -13,8 +13,8 @@ process DUMP_PARAMS {
     val use_centroid
     val min_score
     val skip_downstream
-    val use_iqtree
-    val use_fastme
+    val skip_iqtree
+    val skip_fastme
 
     output:
     tuple val(meta), path("params.yml"), emit: params
@@ -32,8 +32,8 @@ process DUMP_PARAMS {
     use_centroid: ${use_centroid}
     min_score: ${min_score}
     skip_downstream: ${skip_downstream}
-    use_iqtree: ${use_iqtree}
-    use_fastme: ${use_fastme}
+    skip_iqtree: ${skip_iqtree}
+    skip_fastme: ${skip_fastme}
     END_PARAMS
     """
 

modules/local/identify_seq_online.nf

@@ -21,7 +21,7 @@ process IDENTIFY_SEQ_ONLINE {
     prefix = task.ext.prefix ?: meta.id
     """
     fetch_oma_by_sequence.py $fasta id_raw.txt ${prefix}_taxid.txt ${prefix}_exact.txt
-    uniprotize_oma.py id_raw.txt > ${prefix}_id.txt
+    uniprotize_oma_online.py id_raw.txt > ${prefix}_id.txt
 
     cat <<- END_VERSIONS > versions.yml
     "${task.process}":

modules/local/make_report.nf

@@ -54,7 +54,7 @@ process MAKE_REPORT {
     ${task.process}:
         Node: \$(node --version)
         Yarn: \$(yarn --version)
-        React: \$(yarn view react version)
+        React: \$(yarn info react version | cut -d \$'\n' -f 2)
         Python: \$(python --version | cut -d ' ' -f 2)
     END_VERSIONS
     """