Phaseimpute template update and pass first test

.github/CONTRIBUTING.md

@@ -16,15 +16,11 @@ Contributions to the code are even more welcome ;)
 
 If you'd like to write some code for nf-core/phaseimpute, the standard workflow is as follows:
 
-1. Check that there isn't already an issue about your idea in the [nf-core/phaseimpute issues](https://github.com/nf-core/phaseimpute/issues) to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this
 1. Check that there isn't already an issue about your idea in the [nf-core/phaseimpute issues](https://github.com/nf-core/phaseimpute/issues) to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this
 2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [nf-core/phaseimpute repository](https://github.com/nf-core/phaseimpute) to your GitHub account
 3. Make the necessary changes / additions within your forked repository following [Pipeline conventions](#pipeline-contribution-conventions)
 4. Use `nf-core schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10).
 5. Submit a Pull Request against the `dev` branch and wait for the code to be reviewed and merged
-3. Make the necessary changes / additions within your forked repository following [Pipeline conventions](#pipeline-contribution-conventions)
-4. Use `nf-core schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10).
-5. Submit a Pull Request against the `dev` branch and wait for the code to be reviewed and merged
 
 If you're not used to this workflow with git, you can start with some [docs from GitHub](https://help.github.com/en/github/collaborating-with-issues-and-pull-requests) or even their [excellent `git` resources](https://try.github.io/).
 
@@ -41,15 +37,13 @@ Typically, pull-requests are only fully reviewed when these tests are passing, t
 
 There are typically two types of tests that run:
 
-### Lint tests
 ### Lint tests
 
 `nf-core` has a [set of guidelines](https://nf-co.re/developers/guidelines) which all pipelines must adhere to.
 To enforce these and ensure that all pipelines stay in sync, we have developed a helper tool which runs checks on the pipeline code. This is in the [nf-core/tools repository](https://github.com/nf-core/tools) and once installed can be run locally with the `nf-core lint <pipeline-directory>` command.
 
 If any failures or warnings are encountered, please follow the listed URL for more documentation.
 
-### Pipeline tests
 ### Pipeline tests
 
 Each `nf-core` pipeline should be set up with a minimal set of test-data.
@@ -59,7 +53,6 @@ These tests are run both with the latest available version of `Nextflow` and als
 
 ## Patch
 
-:warning: Only in the unlikely and regretful event of a release happening with a bug.
 :warning: Only in the unlikely and regretful event of a release happening with a bug.
 
 - On your own fork, make a new branch `patch` based on `upstream/master`.

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,5 +1,4 @@
 <!--
-<!--
 # nf-core/phaseimpute pull request
 
 Many thanks for contributing to nf-core/phaseimpute!
@@ -12,14 +11,8 @@ Remember that PRs should be made against the dev branch, unless you're preparing
 Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/phaseimpute/tree/master/.github/CONTRIBUTING.md)
 -->
 
-Remember that PRs should be made against the dev branch, unless you're preparing a pipeline release.
-
-Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/phaseimpute/tree/master/.github/CONTRIBUTING.md)
--->
-
 ## PR checklist
 
-- [ ] This comment contains a description of changes (with reason).
 - [ ] This comment contains a description of changes (with reason).
 - [ ] If you've fixed a bug or added code that should be tested, add tests!
 - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/phaseimpute/tree/master/.github/CONTRIBUTING.md)

.github/workflows/branch.yml

@@ -4,18 +4,13 @@ name: nf-core branch protection
 on:
   pull_request_target:
     branches: [master]
-  pull_request_target:
-    branches: [master]
 
 jobs:
   test:
-    runs-on: ubuntu-latest
     runs-on: ubuntu-latest
     steps:
-      # PRs to the nf-core repo master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches
       # PRs to the nf-core repo master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches
       - name: Check PRs
-        if: github.repository == 'nf-core/phaseimpute'
         if: github.repository == 'nf-core/phaseimpute'
         run: |
           { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/phaseimpute ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]

.github/workflows/linting.yml

@@ -2,14 +2,10 @@ name: nf-core linting
 # This workflow is triggered on pushes and PRs to the repository.
 # It runs the `nf-core lint` and markdown lint tests to ensure
 # that the code meets the nf-core guidelines.
-# It runs the `nf-core lint` and markdown lint tests to ensure
-# that the code meets the nf-core guidelines.
 on:
   push:
     branches:
       - dev
-    branches:
-      - dev
   pull_request:
   release:
     types: [published]
@@ -51,7 +47,6 @@ jobs:
           python -m pip install --upgrade pip
           pip install nf-core
 
-
       - name: Run nf-core lint
         env:
           GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}

.gitignore

@@ -6,4 +6,5 @@ results/
 testing/
 testing*
 *.pyc
-*.code-workspace
+*.code-workspace
+.nf-test*

CODE_OF_CONDUCT.md

@@ -45,10 +45,8 @@ Questions, concerns, or ideas on what we can include? Contact members of the Saf
 ## Our Responsibilities
 
 Members of the Safety Team (the Safety Officers) are responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behaviour.
-The safety officer is responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behaviour.
 
 The Safety Team, in consultation with the nf-core core team, have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this CoC, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful.
-The safety officer in consultation with the nf-core core team have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful.
 
 Members of the core team or the Safety Team who violate the CoC will be required to recuse themselves pending investigation. They will not have access to any reports of the violations and will be subject to the same actions as others in violation of the CoC.
 

README.md

@@ -19,17 +19,7 @@
 
 ## Introduction
 
-**nf-core/phaseimpute** is a bioinformatics pipeline that ...
-
-<!-- TODO nf-core:
-   Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the
-   major pipeline sections and the types of output it produces. You're giving an overview to someone new
-   to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction
--->
-
-<!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core
-     workflows use the "tube map" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples.   -->
-<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->
+**nf-core/phaseimpute** is a bioinformatics pipeline to phase and impute genetic data. Different steps are available each corresponding to a dedicated modes.
 
 ### Main steps of the pipeline
 
@@ -43,30 +33,28 @@ The **phaseimpute** pipeline is constituted of 5 main steps:
 > [!NOTE]
 > If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.
 
-<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
-     Explain what rows and columns represent. For instance (please edit as appropriate):
-
+The basic usage of this pipeline is to impute a target dataset based on a phased panel.
 First, prepare a samplesheet with your input data that looks as follows:
 
 `samplesheet.csv`:
 
 ```csv
-sample,fastq_1,fastq_2
-CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz
+sample,bam,bai
+1_BAM_1X,/path/to/.bam,/path/to/.bai
 ```
 
-Each row represents a fastq file (single-end) or a pair of fastq files (paired end).
-
--->
+Each row represents a bam file with its index file.
 
 Now, you can run the pipeline using:
 
-<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->
-
 ```bash
 nextflow run nf-core/phaseimpute \
    -profile <docker/singularity/.../institute> \
    --input samplesheet.csv \
+   --genome "GRCh38" \
+   --panel <phased_reference_panel.vcf.gz> \
+   --steps "impute" \
+   --tools "glimpse1" \
    --outdir <OUTDIR>
 ```
 
@@ -97,11 +85,12 @@ For more details about the output files and reports, please refer to the
 
 ## Credits
 
-nf-core/phaseimpute was originally written by LouisLeNezet.
+nf-core/phaseimpute was originally written by Louis Le Nézet.
 
 We thank the following people for their extensive assistance in the development of this pipeline:
 
-<!-- TODO nf-core: If applicable, make list of people who have also contributed -->
+- Anabella Trigilla
+- Saul Pierotti
 
 ## Contributions and Support
 
@@ -110,7 +99,6 @@ If you would like to contribute to this pipeline, please see the [contributing g
 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)).
 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)).
 
-## Citations
 ## Citations
 
 <!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->

assets/chr_rename_add.txt

@@ -0,0 +1,39 @@
+1 chr1
+2 chr2
+3 chr3
+4 chr4
+5 chr5
+6 chr6
+7 chr7
+8 chr8
+9 chr9
+10 chr10
+11 chr11
+12 chr12
+13 chr13
+14 chr14
+15 chr15
+16 chr16
+17 chr17
+18 chr18
+19 chr19
+20 chr20
+21 chr21
+22 chr22
+23 chr23
+24 chr24
+25 chr25
+26 chr26
+27 chr27
+28 chr28
+29 chr29
+30 chr30
+31 chr31
+32 chr32
+33 chr33
+34 chr34
+35 chr35
+36 chr36
+37 chr37
+38 chr38
+X chrX

assets/panel.csv

@@ -0,0 +1,3 @@
+panel,vcf,index,sites,tsv,legend,phased
+1000GP,1000GP.phased.vcf,1000GP.phased.vcf.csi,1000GP.sites,1000GP.tsv,,TRUE
+1000GP_RePhase,1000GP.vcf,1000GP.vcf.csi,,,,FALSE

assets/samplesheet.csv

@@ -1,3 +1,3 @@
-sample,BAM,BAI
+sample,bam,bai
 1_BAM_1X,/path/to/.bam,/path/to/.bai
 1_BAM_SNP,/path/to/.bam,/path/to/.bai

assets/schema_input.json

@@ -13,17 +13,17 @@
                 "errorMessage": "Sample name must be provided and cannot contain spaces",
                 "meta": ["id"]
             },
-            "BAM": {
+            "bam": {
                 "type": "string",
                 "pattern": "^\\S+\\.bam$",
                 "errorMessage": "BAM file must be provided, cannot contain spaces and must have extension '.bam'"
             },
-            "BAI": {
+            "bai": {
                 "errorMessage": "BAI file must be provided, cannot contain spaces and must have extension '.bai'",
                 "type": "string",
                 "pattern": "^\\S+\\.bai$"
             }
         },
-        "required": ["sample", "BAM", "BAI"]
+        "required": ["sample", "bam", "bai"]
     }
 }

assets/schema_input_panel.json

@@ -0,0 +1,48 @@
+{
+    "$schema": "http://json-schema.org/draft-07/schema",
+    "$id": "https://raw.githubusercontent.com/nf-core/phaseimpute/master/assets/schema_input.json",
+    "title": "nf-core/phaseimpute pipeline - params.input_region schema",
+    "description": "Schema for the file provided with params.input_region",
+    "type": "array",
+    "items": {
+        "type": "object",
+        "properties": {
+            "panel": {
+                "type": "string",
+                "pattern": "^\\S+$",
+                "errorMessage": "Panel name must be provided and cannot contain spaces",
+                "meta": ["panel"]
+            },
+            "vcf": {
+                "type": "string",
+                "pattern": "^\\S+\\.vcf$",
+                "errorMessage": "Panel vcf file must be provided, cannot contain spaces and must have extension '.vcf'"
+            },
+            "index":{
+                "type": "string",
+                "pattern": "^\\S+\\.vcf\\.(tbi|csi)$",
+                "errorMessage": "Panel vcf index file must be provided, cannot contain spaces and must have extension '.vcf.tbi' or '.vcf.csi'"
+            },
+            "sites": {
+                "type": "string",
+                "pattern": "^\\S+\\.sites$",
+                "errorMessage": "Panel sites file must be provided, cannot contain spaces and must have extension '.sites'"
+            },
+            "tsv": {
+                "type": "string",
+                "pattern": "^\\S+\\.tsv$",
+                "errorMessage": "Panel tsv file must be provided, cannot contain spaces and must have extension '.tsv'"
+            },
+            "legend":{
+                "type": "string",
+                "pattern": "^\\S+\\.legend$",
+                "errorMessage": "Panel legend file must be provided, cannot contain spaces and must have extension '.legend'"
+            },
+            "phased": {
+                "type": "boolean",
+                "errorMessage": "Is the vcf given phased? Must be a boolean"
+            }
+        },
+        "required": ["panel", "vcf", "index", "phased"]
+    }
+}

conf/test.config

@@ -22,8 +22,14 @@ params {
     // Input data
     // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
     // TODO nf-core: Give any required params for the test so that command line flags are not needed
-    input  = 'https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv'
+    input  = "../test-datasets/data/bam.csv"
 
     // Genome references
-    genome = 'R64-1-1'
+    fasta    = "../test-datasets/data/reference_genome/21_22/hs38DH.chr21_22.fa"
+    panel    = "https://raw.githubusercontent.com/LouisLeNezet/test-datasets/phaseimpute/data/panel/21_22/1000GP.chr21_22.s.norel.bcf"
+    phased   = true
+
+    // Impute parameters
+    step   = "impute"
+    tools  = "glimpse1"
 }

conf/test_panelprep.config

@@ -21,7 +21,7 @@ params {
 
     // Input data
     input              = "tests/csv/panel.csv"
-    input_region_file  = "tests/csv/regionsheet.csv"
+    input_region       = "tests/csv/regionsheet.csv"
     outdir             = "results/test_panelprep"
     genome             = "GRCh38"
 

docs/development.md

@@ -14,6 +14,30 @@ conda activate nf-core-phaseimpute-1.0dev
 nf-core modules install
 ```
 
+## Run tests
+
+```bash
+nextflow run main.nf -profile singularity,test --outdir results -resume
+```
+
+## Problematic
+
+### Channel management and combination
+
+If only one specie at a time, then only one fasta file and only one map file (normally ?)
+Do we want to be able to compute multiple panel at the same time ?
+If so we need to correctly combine the different channel depending on their meta map.
+
+All channel need to be identified by a meta map as follow:
+
+- I : individual id
+- P : panel id
+- R : region used
+- M : map used
+- T : tool used
+- G : reference genome used (is it needed ?)
+
+
 ## Open questions
 
 How to use different schema ?