Merge pull request #61 from nf-core/fix/relative-path-resolving

Fix relative paths, update containers, update testdata use

.github/workflows/awsfulltest.yml

@@ -15,9 +15,6 @@ jobs:
     steps:
       - name: Launch workflow via tower
         uses: seqeralabs/action-tower-launch@v2
-        # TODO nf-core: You can customise AWS full pipeline tests as required
-        # Add full size test data (but still relatively small datasets for few samples)
-        # on the `test_full.config` test runs with only one set of parameters
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}

.github/workflows/ci.yml

@@ -43,8 +43,5 @@ jobs:
           password: ${{ secrets.GITHUB_TOKEN }}
 
       - name: Run pipeline with test data
-        # TODO nf-core: You can customise CI pipeline run tests as required
-        # For example: adding multiple test runs with different parameters
-        # Remember that you can parallelise this by using strategy.matrix
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results

README.md

@@ -1,5 +1,7 @@
 # ![nf-core/pixelator](docs/images/nf-core-pixelator_logo_light.png#gh-light-mode-only) ![nf-core/pixelator](docs/images/nf-core-pixelator_logo_dark.png#gh-dark-mode-only)
 
+[![nf-core CI](https://github.com/nf-core/pixelator/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/pixelator/actions/workflows/ci.yml)
+[![nf-core linting](https://github.com/nf-core/pixelator/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/pixelator/actions/workflows/linting.yml)
 [![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/pixelator/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
 
 [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/)
@@ -12,22 +14,11 @@
 
 ## Introduction
 
-<!--
-   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
--->
-
 **nf-core/pixelator** is a bioinformatics best-practice analysis pipeline for analysis of Molecular Pixelation assays.
 It takes a samplesheet as input and will process your data using `pixelator` to produce final antibody counts.
 
-<!-- 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.   -->
-
 ![](./docs/images/nf_core_pixelator_metromap.svg)
 
-<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->
-
 1. Build amplicon from input reads ([`pixelator amplicon`](https://github.com/PixelgenTechnologies/pixelator))
 2. Read QC and filtering, correctness of the pixel binding sequence sequences ([`pixelator preqc | pixelator adapterqc`](https://github.com/PixelgenTechnologies/pixelator))
 3. Assign a marker (barcode) to each read ([`pixelator demux`](https://github.com/PixelgenTechnologies/pixelator))
@@ -44,22 +35,6 @@ It takes a samplesheet as input and will process your data using `pixelator` to
 > 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):
-
-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
-```
-
-Each row represents a fastq file (single-end) or a pair of fastq files (paired end).
-
--->
-
 First, prepare a samplesheet with your input data that looks as follows:
 
 `samplesheet.csv`:
@@ -95,7 +70,7 @@ For more details about the output files and reports, please refer to the
 
 ## Credits
 
-nf-core/pixelator was originally written for [Pixelgen Technologies AB](https://www.pixelgen.tech/) by:
+nf-core/pixelator was originally written for [Pixelgen Technologies AB](https://www.pixelgen.com/) by:
 
 - Florian De Temmerman
 - Johan Dahlberg
@@ -114,8 +89,6 @@ For further information or help, don't hesitate to get in touch on the [Slack `#
 <!-- 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. -->
 <!-- If you use  nf-core/pixelator for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->
 
-<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->
-
 An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.
 
 You can cite the `nf-core` publication as follows:

conf/test.config

@@ -23,8 +23,8 @@ params {
     max_memory = '6.GB'
     max_time   = '6.h'
 
-    input  = "https://raw.githubusercontent.com/pixelgentechnologies/test-datasets/pixelator/samplesheet/samplesheet.csv"
-    input_basedir = "s3://pixelgen-technologies-datasets/nf-core-pixelator/testdata/micro/"
+    input  = "https://raw.githubusercontent.com/nf-core/test-datasets/pixelator/samplesheet/samplesheet.csv"
+    input_basedir  = "https://raw.githubusercontent.com/nf-core/test-datasets/pixelator/testdata"
 
     multiplet_recovery = true
     min_size = 2

modules/local/pixelator/collect_metadata.nf

@@ -9,7 +9,7 @@ process PIXELATOR_COLLECT_METADATA {
     cache false
 
     conda "bioconda::pixelator=0.13.1"
-    container "biocontainers/pixelator:0.13.1"
+    container "biocontainers/pixelator:0.13.1--pyh7cba7a3_0"
 
     input:
 

modules/local/pixelator/list_options.nf

@@ -3,7 +3,7 @@ process PIXELATOR_LIST_OPTIONS {
 
 
     conda "bioconda::pixelator=0.13.1"
-    container "biocontainers/pixelator:0.13.1"
+    container "biocontainers/pixelator:0.13.1--pyh7cba7a3_0"
 
     output:
     path "design_options.txt"     , emit: designs

modules/local/pixelator/single-cell/amplicon/main.nf

@@ -4,7 +4,7 @@ process PIXELATOR_AMPLICON {
 
 
     conda "bioconda::pixelator=0.13.1"
-    container "biocontainers/pixelator:0.13.1"
+    container "biocontainers/pixelator:0.13.1--pyh7cba7a3_0"
 
     input:
     tuple val(meta), path(reads)

modules/local/pixelator/single-cell/analysis/main.nf

@@ -4,7 +4,7 @@ process PIXELATOR_ANALYSIS {
 
 
     conda "bioconda::pixelator=0.13.1"
-    container "biocontainers/pixelator:0.13.1"
+    container "biocontainers/pixelator:0.13.1--pyh7cba7a3_0"
 
     input:
     tuple val(meta), path(data)

modules/local/pixelator/single-cell/annotate/main.nf

@@ -4,7 +4,7 @@ process PIXELATOR_ANNOTATE {
 
 
     conda "bioconda::pixelator=0.13.1"
-    container "biocontainers/pixelator:0.13.1"
+    container "biocontainers/pixelator:0.13.1--pyh7cba7a3_0"
 
     input:
     tuple val(meta), path(dataset), path(panel_file), val(panel)

modules/local/pixelator/single-cell/collapse/main.nf

@@ -3,7 +3,7 @@ process PIXELATOR_COLLAPSE {
     label 'process_medium'
 
     conda "bioconda::pixelator=0.13.1"
-    container "biocontainers/pixelator:0.13.1"
+    container "biocontainers/pixelator:0.13.1--pyh7cba7a3_0"
 
     input:
     tuple val(meta), path(reads), path(panel_file), val(panel)

modules/local/pixelator/single-cell/demux/main.nf

@@ -4,7 +4,7 @@ process PIXELATOR_DEMUX {
 
 
     conda "bioconda::pixelator=0.13.1"
-    container "biocontainers/pixelator:0.13.1"
+    container "biocontainers/pixelator:0.13.1--pyh7cba7a3_0"
 
     input:
     tuple val(meta), path(reads), path(panel_file), val(panel)

modules/local/pixelator/single-cell/graph/main.nf

@@ -4,7 +4,7 @@ process PIXELATOR_GRAPH {
 
 
     conda "bioconda::pixelator=0.13.1"
-    container "biocontainers/pixelator:0.13.1"
+    container "biocontainers/pixelator:0.13.1--pyh7cba7a3_0"
 
     input:
     tuple val(meta), path(edge_list)

modules/local/pixelator/single-cell/qc/main.nf

@@ -4,7 +4,7 @@ process PIXELATOR_QC {
 
 
     conda "bioconda::pixelator=0.13.1"
-    container "biocontainers/pixelator:0.13.1"
+    container "biocontainers/pixelator:0.13.1--pyh7cba7a3_0"
 
     input:
     tuple val(meta), path(reads)

modules/local/pixelator/single-cell/report/main.nf

@@ -4,7 +4,7 @@ process PIXELATOR_REPORT {
 
 
     conda "bioconda::pixelator=0.13.1"
-    container "biocontainers/pixelator:0.13.1"
+    container "biocontainers/pixelator:0.13.1--pyh7cba7a3_0"
 
     input:
     tuple val(meta), path(panel_file), val(panel)

nextflow_schema.json

@@ -16,6 +16,7 @@
                     "type": "string",
                     "format": "file-path",
                     "schema": "assets/schema_input.json",
+                    "mimetype": "text/csv",
                     "exists": true,
                     "pattern": "^\\S+\\.(csv|tsv)$",
                     "description": "Path to comma-separated file containing information about the samples in the experiment.",

subworkflows/local/input_check.nf

@@ -139,8 +139,8 @@ def get_data_basedir(URI samplesheet, String input_basedir) {
     if (uri.getScheme() != null) {
         if (!uri.path.endsWith('/')) {
             def newUrl = new URI(
-                    uri.getProtocol(), uri.getUserInfo(), uri.getHost(),
-                    uri.getPort(), uri.getPath() + '/', url.getQuery(), url.getRef()
+                    uri.getScheme(), uri.getUserInfo(), uri.getHost(),
+                    uri.getPort(), uri.getPath() + '/', uri.getQuery(), uri.getFragment()
             )
             return newUrl
         }