Fix linting and local sbwf

CHANGELOG.md

@@ -47,6 +47,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#274](https://github.com/nf-core/phaseimpute/pull/274) - Fix issue with compressed reference genome by adding `.gzi` file for `BCFTOOLS_MPILEUP`
 - [#275](https://github.com/nf-core/phaseimpute/pull/275) - Fix nf-test errors with latest-everything.
 - [#281](https://github.com/nf-core/phaseimpute/pull/281) - Fix `diffchr()` function.
+- [#293](https://github.com/nf-core/phaseimpute/pull/293) - Fix nf-core and nextflow linting.
 
 ### `Dependencies`
 

README.md

@@ -106,7 +106,7 @@ We thank the following people for their extensive assistance in the development
 
 ## Contributions and Support
 
-If you would like to contribute to this pipeline, please see the [contributing guidelines](docs/CONTRIBUTING.md). Further development tips can be found in the [development documentation](docs/development.md).
+If you would like to contribute to this pipeline, please see the [contributing guidelines](docs/CONTRIBUTING.md).
 
 For further information or help, don't hesitate to get in touch on the [Slack `#phaseimpute` channel](https://nfcore.slack.com/channels/phaseimpute) (you can join with [this invite](https://nf-co.re/join/slack)).
 

assets/methods_description_template.yml

@@ -3,8 +3,6 @@ description: "Suggested text and references to use when describing pipeline usag
 section_name: "nf-core/phaseimpute Methods Description"
 section_href: "https://github.com/nf-core/phaseimpute"
 plot_type: "html"
-## TODO nf-core: Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
-## You inject any metadata in the Nextflow '${workflow}' object
 data: |
   <h4>Methods</h4>
   <p>Data was processed using nf-core/phaseimpute v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (<a href="https://doi.org/10.1038/s41587-020-0439-x">Ewels <em>et al.</em>, 2020</a>), utilising reproducible software environments from the Bioconda (<a href="https://doi.org/10.1038/s41592-018-0046-7">Grüning <em>et al.</em>, 2018</a>) and Biocontainers (<a href="https://doi.org/10.1093/bioinformatics/btx192">da Veiga Leprevost <em>et al.</em>, 2017</a>) projects.</p>

docs/CONTRIBUTING.md

@@ -182,4 +182,33 @@ If you update images or graphics, follow the nf-core [style guidelines](https://
 
 ## Pipeline specific contribution guidelines
 
-<!-- TODO nf-core: Add any pipeline specific contribution guidelines here, such as coding styles, procedures, checklists etc. -->
+`nf-core/phaseimpute` pipeline aim to strictly follow latest nextflow and nf-core guidelines.
+As such, each local modules and subworkflow should be properly written and unittested with nf-test.
+
+Local components should only be considered when they use are specific for this pipeline.
+Otherwise, they should be part of the `nf-core/modules` repository.
+
+### Channel management and combination
+
+All channels need to be identified by a meta map. To follow which information is available, the `meta` argument
+is suffixed with a combination of the following capital letters:
+
+- I : individual id
+- P : panel id
+- R : region used
+- M : map used
+- T : tool used
+- G : reference genome used (is it needed ?)
+- S : simulation (depth or genotype array)
+
+Therefore, the following channel operation example includes a meta map containing the panel id with the region and tool used:
+
+```nextflow
+ch_panel_for_impute.map {
+    metaPRT, vcf, index -> ...
+}
+```
+
+### Release names
+
+The names of releases are composed of a color and a dog breed.

modules/local/addcolumns/meta.yml

@@ -0,0 +1,61 @@
+name: addcolumns
+description: Add metadata information to an existing file as additional columns
+keywords:
+  - columns
+  - metadata
+  - awk
+tools:
+  - gawk:
+      description: "GNU awk"
+      homepage: "https://www.gnu.org/software/gawk/"
+      documentation: "https://www.gnu.org/software/gawk/manual/"
+      tool_dev_url: "https://www.gnu.org/prep/ftp.html"
+      licence:
+        - "GPL v3"
+      identifier: ""
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        The following keys are added in additional columns to the input file.
+        e.g. [ id:'test', depth:1, gparray:'illumina', tools:'glimpse', panel:'1000G' ]
+  - input:
+      type: file
+      description: Textual format file
+output:
+  txt:
+    - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - txt:
+        type: file
+        description: Resulting file with additional columns containing the metadata information
+        pattern: "*.txt"
+  versions_gawk:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - gawk:
+          type: string
+          description: The name of the tool
+      - awk -Wversion | sed '1!d; s/.*Awk //; s/,.*//':
+          type: eval
+          description: The expression to obtain the version of the tool
+topics:
+  versions:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - gawk:
+          type: string
+          description: The name of the tool
+      - awk -Wversion | sed '1!d; s/.*Awk //; s/,.*//':
+          type: eval
+          description: The expression to obtain the version of the tool
+authors:
+  - "@louislenezet"
+maintainers:
+  - "@louislenezet"

modules/local/listtofile/meta.yml

@@ -4,11 +4,14 @@ keywords:
   - list
   - gawk
 tools:
-  - annotate:
-      description: |
-        Extract the file names from a list of path and register them into a file.
-        The corresponding identifier can be added to the file in a second column
-        or in a separate file.
+  - gawk:
+      description: "GNU awk"
+      homepage: "https://www.gnu.org/software/gawk/"
+      documentation: "https://www.gnu.org/software/gawk/manual/"
+      tool_dev_url: "https://www.gnu.org/prep/ftp.html"
+      licence:
+        - "GPL v3"
+      identifier: ""
 input:
   - - meta:
         type: map

modules/local/vcfchrextract/meta.yml

@@ -6,12 +6,14 @@ keywords:
   - head
   - contig
 tools:
-  - head:
-      description: Extract header from variant calling file.
+  - query:
+      description: |
+        Extracts fields from VCF or BCF files and outputs them in user-defined format.
       homepage: http://samtools.github.io/bcftools/bcftools.html
-      documentation: https://samtools.github.io/bcftools/bcftools.html#head
+      documentation: http://www.htslib.org/doc/bcftools.html
       doi: 10.1093/bioinformatics/btp352
       licence: ["MIT"]
+      identifier: biotools:bcftools
 input:
   - meta:
       type: map

subworkflows/local/prepare_genome/main.nf

@@ -20,23 +20,23 @@ workflow PREPARE_GENOME {
         []
     ])
 
+    def need_faidx = !fasta_fai_path || (is_compressed && !fasta_gzi_path)
+    if (need_faidx) {
+        SAMTOOLS_FAIDX(ch_fasta, false)
+    }
+
     if (fasta_fai_path) {
         ch_fai = channel.of(file(fasta_fai_path, checkIfExists:true))
     } else {
-        SAMTOOLS_FAIDX(ch_fasta, false)
         ch_fai = SAMTOOLS_FAIDX.out.fai.map{ _meta, fasta_fai -> fasta_fai }
     }
-    if (is_compressed) {
-        if (fasta_gzi_path) {
-            ch_gzi = channel.of(file(fasta_gzi_path, checkIfExists:true))
-        } else if (!fasta_fai_path) {
-            ch_gzi = SAMTOOLS_FAIDX.out.gzi.map{ _meta, gzi -> gzi }
-        } else {
-            SAMTOOLS_FAIDX(ch_fasta, false)
-            ch_gzi = SAMTOOLS_FAIDX.out.gzi.map{ _meta, gzi -> gzi }
-        }
+
+    if (!is_compressed) {
+        ch_gzi = channel.of([[]])
+    } else if (fasta_gzi_path) {
+        ch_gzi = channel.of(file(fasta_gzi_path, checkIfExists:true))
     } else {
-        ch_gzi = channel.of([])
+        ch_gzi = SAMTOOLS_FAIDX.out.gzi.map{ _meta, gzi -> gzi }
     }
 
     ch_fasta_fai_gzi = ch_fasta
@@ -46,5 +46,5 @@ workflow PREPARE_GENOME {
         .collect()
 
     emit:
-    ch_fasta_fai_gzi
+    ch_fasta_fai_gzi = ch_fasta_fai_gzi
 }

subworkflows/local/prepare_genome/meta.yml

@@ -0,0 +1,51 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
+name: "PREPARE_GENOME"
+description: |
+  Subworkflow to prepare the reference genome for imputation.
+  This includes indexing the genome and preparing the necessary files.
+keywords:
+  - genome
+  - reference
+  - indexing
+components:
+  - samtools/faidx
+input:
+  - genome:
+      type: string
+      description: Reference genome name
+  - fasta_path:
+      type: file
+      description: Reference genome FASTA file
+      pattern: "*.{fa,fasta,fa.gz,fasta.gz}"
+  - fasta_index_path:
+      type: file
+      description: Reference genome FASTA index file
+      pattern: "*.{fai,faidx}"
+  - fasta_gzi_path:
+      type: file
+      description: Reference genome FASTA gzi index file (optional)
+      pattern: "*.gzi"
+output:
+  - ch_fasta_fai_gzi:
+      type: channel
+      description: Channel containing the reference genome FASTA file, its index and gzi index if present
+      structure:
+        - meta:
+            type: map
+            description: Metadata map that will be combined with the input data map
+        - fasta:
+            type: file
+            description: Reference genome FASTA file
+            pattern: "*.{fa,fasta,fa.gz,fasta.gz}"
+        - fai:
+            type: file
+            description: Reference genome FASTA index file
+            pattern: "*.{fai,faidx}"
+        - gzi:
+            type: file
+            description: Reference genome FASTA gzi index file (optional)
+            pattern: "*.gzi"
+authors:
+  - "@louislenezet"
+maintainers:
+  - "@louislenezet"