Realease review jose fixes

.github/workflows/ci_master.yml

@@ -34,7 +34,7 @@ jobs:
           - "test"
           - "test_conda"
           - "test_pdb"
-          - "test_nosheet"
+          - "test_no_sheet"
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4

.nf-core.yml

@@ -2,15 +2,14 @@ lint:
   files_exist:
     - conf/igenomes.config
     - conf/igenomes_ignored.config
-    - .github/PULL_REQUEST_TEMPLATE.md
   files_unchanged:
     - .github/CONTRIBUTING.md
   multiqc_config: false
   actions_ci: false # TODO: remove this with nf-core template version 3.3.0
 nf_core_version: 3.2.0
 repository_type: pipeline
 template:
-  author: Luisa Santus, Jose Espinosa Carrasco
+  author: Luisa Santus, Jose Espinosa-Carrasco
   description: Pipeline to run and benchmark multiple sequence alignment tools.
   force: false
   is_nfcore: true

CHANGELOG.md

@@ -7,7 +7,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 Nova Icaria is a beach in Barcelona. We started from Somorrostro (beach in front of CRG) and we are going up the way to Costa Brava.
 
-Minor release of nf-coremultiplesequencealign/.
+Minor release of nf-core/multiplesequencealign.
 
 This fixes few bugs, improves the documentation and adds the possibility to avoid the samplesheet and toolsheet and pass direclty the input files and tools directives.
 

docs/output.md

@@ -59,7 +59,7 @@ All paths are relative to the top-level results directory.
         - <code>perc_sim/\*.txt</code>: file containing the pairwise sequence similarity for all input sequences. If <code>--calc_sim</code> is specified.
       - <code>structures/</code>
         - <code>plddt/\*\_full_plddt.csv</code>: file containing the plddt of the structures for each sequence in the input file. If <code>--extract_plddt</code> is specified.
-        </details>
+      </details>
 
     - <details markdown="1">
         <summary><code>summary/</code></summary>

docs/usage.md

@@ -73,17 +73,15 @@ FAMSA,,REGRESSIVE,
 
 More examples [here](https://github.com/nf-core/test-datasets/tree/multiplesequencealign/toolsheet).
 
-:::note
-Each of the trees and aligners are available as standalones. You can leave `args_tree` and `args_aligner` empty if you are cool with the default settings of each method. Alternatively, you can leave `args_tree` empty to use the default guide tree with each aligner.
-:::
+> [!NOTE]
+> Each of the trees and aligners are available as standalones. You can leave `args_tree` and `args_aligner` empty if you are cool with the default settings of each method. Alternatively, you can leave `args_tree` empty to use the default guide tree with each aligner.
 
-:::note
-use the exact spelling as listed below in [align](#3-align) and [guide trees](#2-guide-trees)!
-:::
+> [!NOTE]
+> Use the exact spelling as listed below in [align](#3-align) and [guide trees](#2-guide-trees)!
 
 `tree` is the tool used to build the tree (optional).
 
-Arguments to the tree tool can be provided using `args_tree`. Please refer to each tool's documentation (optional).
+Arguments to the tree tool can be provided using `args_tree` (optional). Please refer to each tool's documentation.
 
 The `aligner` column contains the tool to run the alignment (optional).
 
@@ -194,7 +192,7 @@ The provided structures (see samplesheet) are used to evaluate the quality of th
 Finally, a summary table with all the computed statistics and evaluations is reported in MultiQC (skip by using `--skip_multiqc`).
 Moreover, a Shiny app is generated with interactive summary plots (skip with `--skip_shiny`).
 
-If structures are provided, the [Foldmason](https://github.com/steineggerlab/foldmason) visualizatin will be rendered (skip with `--skip_visualisation`).
+If structures are provided, the [Foldmason](https://github.com/steineggerlab/foldmason) visualisation will be rendered (skip with `--skip_visualisation`).
 
 :::warning
 You will need to have [Shiny](https://shiny.posit.co/py/) installed to run it! See [output documentation](https://nf-co.re/multiplesequencealign/output) for more info.

docs/usage/FAQs.md

@@ -24,7 +24,7 @@ The flag <code>--skip_pdbcoversion</code> false will make sure that the fasta fi
 
 </details>
 
-### USECASES
+### USE CASES
 
 <details>
   <summary> I want to deploy one tool on one dataset. I am not interested in any evaluation, report etc. </summary>

docs/usage/chaining_with_proteinfold.md

@@ -4,7 +4,7 @@ Structural aligners leverage protein structural information to compute MSAs.
 
 You can provide your PDB structures via the samplesheet, as outlined in the primary usage documentation. However, if you do not already have protein structures available, you may opt to use protein structure prediction tools to create these models.
 
-To facilitate this, we offer an integration with the nf-core/proteinfold pipeline, enabling you to generate the protein structures required for this workflow.
+To facilitate this, we offer an integration with the [nf-core/proteinfold](https://github.com/nf-core/proteinfold) pipeline, enabling you to generate the protein structures required for this workflow.
 
 To do so, you only need to build one samplesheet file, in the exact format required by nf-core/multiplesequencealign pipeline.
 This is made compatible with nf-core/proteinfold and will predict and output the structures in the format required by the nf-core/multiplesquencealign pipeline.
@@ -40,7 +40,7 @@ nextflow run nf-core/multiplesequencealign \
 ```
 
 > [!NOTE]
-> The one imporant parameter NOT to forget in proteinfold for the chaining is `--split_fasta`. This will allow to use a multifasta file as input for monomer predictions, needed by the MSA pipeline.The rest of the proteinfold parameters can and should be tuned according to your preferences for your proteinfold run. Please refer to the proteinfold documentation for this.
+> The one important parameter NOT to forget in proteinfold for the chaining is `--split_fasta`. This will allow to use a multifasta file as input for monomer predictions, needed by the MSA pipeline.The rest of the proteinfold parameters can and should be tuned according to your preferences for your proteinfold run. Please refer to the proteinfold documentation for this.
 
 > [!WARNING]
 > This is currently an experimetal feature and only available in the dev branch of proteinfold, so also do not forget `-r dev`. This feature will be soon available with the next release of nf-core/proteinfold.

nextflow.config

@@ -123,11 +123,7 @@ profiles {
     }
     docker {
         docker.enabled          = true
-        if (params.use_gpu) {
-            docker.runOptions = '--gpus all'
-        } else {
-            docker.runOptions      = '-u $(id -u):$(id -g)'
-        }
+        docker.runOptions      = params.use_gpu ? '--gpus all' : '-u $(id -u):$(id -g)'
         conda.enabled           = false
         singularity.enabled     = false
         podman.enabled          = false
@@ -137,16 +133,12 @@ profiles {
         docker.runOptions       = '-u $(id -u):$(id -g)'
     }
     arm {
-        if (params.use_gpu) {
-            docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64 --gpus all'
-        } else {
-            docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64'
-        }
+        docker.runOptions     = params.use_gpu ? '-u $(id -u):$(id -g) --platform=linux/amd64 --gpus all' : '-u $(id -u):$(id -g) --platform=linux/amd64'
     }
     singularity {
         singularity.enabled     = true
         singularity.autoMounts  = true
-        if (params.use_gpu) { singularity.runOptions = '--nv' }
+        singularity.runOptions = params.use_gpu ? '--nv' : singularity.runOptions
         conda.enabled           = false
         docker.enabled          = false
         podman.enabled          = false
@@ -185,6 +177,7 @@ profiles {
     apptainer {
         apptainer.enabled       = true
         apptainer.autoMounts    = true
+        apptainer.runOptions    = params.use_gpu ? '--nv' : apptainer.runOptions
         conda.enabled           = false
         docker.enabled          = false
         singularity.enabled     = false
@@ -215,7 +208,7 @@ profiles {
     test_full               { includeConfig 'conf/test_full.config'         }
     test_tiny               { includeConfig 'conf/test_tiny.config'         }
     test_pdb                { includeConfig 'conf/test_pdb.config'          }
-    test_nosheet            { includeConfig 'conf/test_nosheet.config'      }
+    test_nosheet            { includeConfig 'conf/test_no_sheet.config'      }
     test_conda              { includeConfig 'conf/test_conda.config'        }
     easy_deploy             { includeConfig 'conf/easy_deploy.config'       }
 }
@@ -296,7 +289,7 @@ manifest {
         [
             name: ' Jose Espinosa Carrasco',
             affiliation: 'Centre for Genomic Regulation (CRG)',
-            email: '[email protected]',
+            email: '[email protected]',
             github: '@joseespinosa',
             contribution: ['author', 'maintainer', 'contributor'],
             orcid: 'https://orcid.org/0000-0002-1541-042X'

subworkflows/local/STATS/main.nf

@@ -1,14 +1,14 @@
 //
 // Compute stats about the input sequences
 //
-include {   CALCULATE_SEQSTATS                             } from '../../../modules/local/custom/calculate_seqstats'
-include {   PARSE_SIM                                      } from '../../../modules/local/custom/parse_sim'
-include {   EXTRACT_PLDDT                                  } from '../../../modules/local/custom/extract_plddt'
-include {   TCOFFEE_SEQREFORMAT as TCOFFEE_SEQREFORMAT_SIM } from '../../../modules/nf-core/tcoffee/seqreformat/main.nf'
-include {   CSVTK_CONCAT  as CONCAT_SEQSTATS               } from '../../../modules/nf-core/csvtk/concat/main.nf'
-include {   CSVTK_CONCAT  as CONCAT_SIMSTATS               } from '../../../modules/nf-core/csvtk/concat/main.nf'
-include {   CSVTK_CONCAT  as CONCAT_PLDDTS                 } from '../../../modules/nf-core/csvtk/concat/main.nf'
-include {   CSVTK_JOIN    as MERGE_STATS                   } from '../../../modules/nf-core/csvtk/join/main.nf'
+include { CALCULATE_SEQSTATS                             } from '../../../modules/local/custom/calculate_seqstats'
+include { PARSE_SIM                                      } from '../../../modules/local/custom/parse_sim'
+include { EXTRACT_PLDDT                                  } from '../../../modules/local/custom/extract_plddt'
+include { TCOFFEE_SEQREFORMAT as TCOFFEE_SEQREFORMAT_SIM } from '../../../modules/nf-core/tcoffee/seqreformat/main.nf'
+include { CSVTK_CONCAT  as CONCAT_SEQSTATS               } from '../../../modules/nf-core/csvtk/concat/main.nf'
+include { CSVTK_CONCAT  as CONCAT_SIMSTATS               } from '../../../modules/nf-core/csvtk/concat/main.nf'
+include { CSVTK_CONCAT  as CONCAT_PLDDTS                 } from '../../../modules/nf-core/csvtk/concat/main.nf'
+include { CSVTK_JOIN    as MERGE_STATS                   } from '../../../modules/nf-core/csvtk/join/main.nf'
 
 workflow STATS {
     take:

subworkflows/local/TEMPLATES/main.nf

@@ -9,7 +9,7 @@ workflow TEMPLATES {
 
     main:
 
-    ch_versions     = Channel.empty()
+    ch_versions = Channel.empty()
 
     ch_optional_data_template = ch_optional_data.join(ch_templates, by:0, remainder:true)
     ch_optional_data_template

workflows/multiplesequencealign.nf

@@ -60,16 +60,15 @@ workflow MULTIPLESEQUENCEALIGN{
     ch_tools    // channel: [ val(guide_tree_tool), val(args_guide_tree_tool), val(alignment_tool), val(args_alignment_tool) ]
 
     main:
-    ch_multiqc_files                = Channel.empty()
-    ch_multiqc_report               = Channel.empty()
-    evaluation_summary              = Channel.empty()
-    stats_summary                   = Channel.empty()
-    stats_and_evaluation_summary    = Channel.empty()
-    ch_refs                         = Channel.empty()
-    ch_templates                    = Channel.empty()
-    ch_optional_data                = Channel.empty()
-    ch_versions                     = Channel.empty()
-
+    ch_multiqc_files             = Channel.empty()
+    ch_multiqc_report            = Channel.empty()
+    evaluation_summary           = Channel.empty()
+    stats_summary                = Channel.empty()
+    stats_and_evaluation_summary = Channel.empty()
+    ch_refs                      = Channel.empty()
+    ch_templates                 = Channel.empty()
+    ch_optional_data             = Channel.empty()
+    ch_versions                  = Channel.empty()
 
     ch_input
         .filter { it[1].size() > 0}
@@ -140,13 +139,13 @@ workflow MULTIPLESEQUENCEALIGN{
         // otherwise, map the optional_data to the sequence IDs provided by the
         // various fasta files
         // *****************************************************************
-        if(!params.seqs){
+        if(!params.seqs) {
             optional_data_to_be_mapped
                 .map { it -> [ [ id: params.pdbs_dir.split("/")[-1].split("\\.")[0] ], it ] }
                 .groupTuple(by: 0)
                 .set { ch_optional_data }
 
-        }else{
+        } else {
             // Identify the sequence IDs from the input fasta file(s)
             ch_seqs.splitFasta(record: [ id: true ] )
                 .map { id, seq_id -> [ seq_id, id ] }