Merge pull request #164 from LouisLeNezet/dev

Update documentation and miscellanous modification for release

CHANGELOG.md

@@ -3,10 +3,10 @@
 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).
 
-## v1.0.0 - Black Labrador [2024-10-28]
+## v1.0.0 - Black Labrador [2024-11-30]
 
 Initial release of nf-core/phaseimpute, created with the [nf-core](https://nf-co.re/) template.
-Special thanks to [Matthias Hörtenhuber](https://github.com/mashehu) and [Mazzalab](https://github.com/mazzalab) for the review of this release.
+Special thanks to [Matthias Hörtenhuber](https://github.com/mashehu), [Mazzalab](https://github.com/mazzalab) and [Sofia Stamouli](https://github.com/sofstam) for the review of this release.
 
 ### `Added`
 
@@ -25,6 +25,7 @@ Special thanks to [Matthias Hörtenhuber](https://github.com/mashehu) and [Mazza
 - [#131](https://github.com/nf-core/phaseimpute/pull/131) - Set normalisation as optional. Fix extension detection function. Add support for validation with vcf files. Concatenate vcf only if more than one file. Change `--phased` to `--phase` for consistency.
 - [#143](https://github.com/nf-core/phaseimpute/pull/143) - Improve contigs warning and error logging. The number of chromosomes contigs is summarized if above `max_chr_names`.
 - [#146](https://github.com/nf-core/phaseimpute/pull/146) - Add `seed` parameter for `QUILT`.
+- [#164](https://github.com/nf-core/phaseimpute/pull/164) - Add additional requirement on input schema `"uniqueEntries": ["panel", "chr"]` and `end` should be greater than `start` in regions.
 
 ### `Changed`
 
@@ -65,6 +66,7 @@ Special thanks to [Matthias Hörtenhuber](https://github.com/mashehu) and [Mazza
 - [#157](https://github.com/nf-core/phaseimpute/pull/157) - Add `chunk_model` as parameter for better control over `GLIMPSE2_CHUNK` and set window size in `GLIMPSE1_CHUNK` and `GLIMPSE2_chunk` to 4mb to reduce number of chunks (empirical).
 - [#160](https://github.com/nf-core/phaseimpute/pull/160) - Improve `CHANGELOG.md` and add details to `usage.md`
 - [#158](https://github.com/nf-core/phaseimpute/pull/158) - Remove frequency computation and phasing from full test to reduce cost and computational time.
+- [#164](https://github.com/nf-core/phaseimpute/pull/164) - Rename `BAM_REGION_SAMTOOLS` to `BAM_EXTRACT_REGION_SAMTOOLS`. Remove `GLIMPSE2_SPLITREFERENCE` as it is not used. Add more steps to `test_all` profile for more exhaustivity.
 
 ### `Fixed`
 
@@ -78,6 +80,7 @@ Special thanks to [Matthias Hörtenhuber](https://github.com/mashehu) and [Mazza
 - [#153](https://github.com/nf-core/phaseimpute/pull/153) - Fix getFileExtension function. Fix image in `usage.md`. Fix small warnings and errors with updated language server. `def` has been added when necessary, `:` use instead of `,` in assertions, `_` added to variables not used in closures, `for` loop replaced by `.each{}`, remove unused code / input.
 - [#161](https://github.com/nf-core/phaseimpute/pull/161) - Fix `VCF_SPLIT_BCFTOOLS` when only one sample present by updating `BCFTOOLS_PLUGINSPLIT` and adding `BCFTOOLS_QUERY` to get truth samples names for renaming the resulting files.
 - [#162](https://github.com/nf-core/phaseimpute/pull/162) - Fix `fai` usage when provided by `genomes` parameter.
+- [#164](https://github.com/nf-core/phaseimpute/pull/164) - Improve documentation writing
 
 ### `Dependencies`
 
@@ -110,3 +113,4 @@ Special thanks to [Matthias Hörtenhuber](https://github.com/mashehu) and [Mazza
 [Nicolas Schcolnicov](https://github.com/nschcolnicov)
 [Hemanoel Passarelli](https://github.com/hemanoel)
 [Matthias Hörtenhuber](https://github.com/mashehu)
+[Sofia Stamouli](https://github.com/sofstam)

README.md

@@ -21,7 +21,7 @@
 
 **nf-core/phaseimpute** is a bioinformatics pipeline to phase and impute genetic data.
 
-<img src="docs/images/metro/phaseimpute.drawio.png" alt="metromap"/>
+<img src="docs/images/metro/MetroMap_animated.svg" alt="metromap"/>
 
 The whole pipeline consists of five main steps, each of which can be run separately and independently. Users are not required to run all steps sequentially and can select specific steps based on their needs:
 
@@ -103,7 +103,7 @@ 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](.github/CONTRIBUTING.md).
+If you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md). Further development tips can be found in the [development documentation](docs/development.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/schema_chunks.json

@@ -25,6 +25,7 @@
                 "errorMessage": "File with chunks per chromosome must be provided. Must have .txt or .bin extension"
             }
         },
-        "required": ["panel", "chr", "file"]
+        "required": ["panel", "chr", "file"],
+        "uniqueEntries": ["panel", "chr"]
     }
 }

assets/schema_input_panel.json

@@ -30,6 +30,7 @@
                 "errorMessage": "Panel index file must be provided, cannot contain spaces and must have extension '.vcf' or '.bcf' with optional '.gz' extension and with '.csi' or '.tbi' extension"
             }
         },
-        "required": ["panel", "chr", "vcf", "index"]
+        "required": ["panel", "chr", "vcf", "index"],
+        "uniqueEntries": ["panel", "chr"]
     }
 }

assets/schema_map.json

@@ -16,7 +16,7 @@
             "map": {
                 "type": "string",
                 "pattern": "^\\S+\\.(g)?map(\\.gz)?$",
-                "errorMessage": "Map file must be provided, cannot contain spaces and must have extension '.map' or '.gmap' with optional 'gz' extension"
+                "errorMessage": "Map file must be provided, cannot contain spaces and must have extension '.map' or '.gmap' with optional '.gz' extension"
             }
         },
         "required": ["chr", "map"]

assets/schema_posfile.json

@@ -40,6 +40,7 @@
                 "errorMessage": "Legend file can be provided, cannot contain spaces and must have extension '.legend' with '.gz' extension"
             }
         },
-        "required": ["panel", "chr"]
+        "required": ["panel", "chr"],
+        "uniqueEntries": ["panel", "chr"]
     }
 }

conf/steps/chrcheck.config

@@ -30,6 +30,6 @@ process {
     }
 
     withName: 'NFCORE_PHASEIMPUTE:CHRCHECK_.*:VCF_CHR_RENAME_BCFTOOLS:BCFTOOLS_ANNOTATE' {
-        ext.args   = ["-Oz", "--no-version", "--write-index=tbi"].join(' ')
+        ext.args = ["-Oz", "--no-version", "--write-index=tbi"].join(' ')
     }
 }

conf/steps/panel_prep.config

@@ -206,14 +206,4 @@ process {
         ]
     }
 
-    withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_CHUNK_GLIMPSE:GLIMPSE2_SPLITREFERENCE' {
-        ext.prefix    = { "${meta.id}_${meta.chr}_chunks_glimpse2" }
-        publishDir = [
-            path: { "${params.outdir}/prep_panel/chunks/glimpse2/" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
-            enabled: true
-        ]
-    }
-
 }

conf/steps/simulation.config

@@ -12,20 +12,20 @@
 
 process {
     // Optional subworkflow to extract regions
-    withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:BAM_REGION_SAMTOOLS:.*' {
+    withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:BAM_EXTRACT_REGION_SAMTOOLS:.*' {
         publishDir = [ enabled: false ]
         tag = {"${meta.id} ${meta.chr}"}
     }
-    withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:BAM_REGION_SAMTOOLS:SAMTOOLS_VIEW' {
+    withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:BAM_EXTRACT_REGION_SAMTOOLS:SAMTOOLS_VIEW' {
         ext.args   = ["--output-fmt bam", "--write-index"].join(' ')
         ext.prefix = { "${meta.id}_R${meta.region.replace(':','_')}" }
     }
 
-    withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:BAM_REGION_SAMTOOLS:SAMTOOLS_MERGE' {
+    withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:BAM_EXTRACT_REGION_SAMTOOLS:SAMTOOLS_MERGE' {
         ext.prefix = { "${meta.id}" }
         tag = {"${meta.id} ${meta.chr}"}
     }
-    withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:BAM_REGION_SAMTOOLS:SAMTOOLS_INDEX' {
+    withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:BAM_EXTRACT_REGION_SAMTOOLS:SAMTOOLS_INDEX' {
         ext.args = ""
     }
 

conf/test_all.config

@@ -29,11 +29,14 @@ params {
 
     // Genome references
     fasta        = params.pipelines_testdata_base_path + "hum_data/reference_genome/GRCh38.s.fa.gz"
+
+    // Panel preparation
     panel        = "${projectDir}/tests/csv/panel.csv"
     phase        = true
     normalize    = true
-    compute_freq = false
+    compute_freq = true
     chunk_model  = "recursive"
+    remove_samples = "NA12878,NA12891,NA12892"
 
     // Pipeline steps
     steps = "all"

docs/development.md

@@ -0,0 +1,26 @@
+# Tips for development
+
+## 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.