From 88ed15285e5757cc3833a7a57b928a9af1b81af5 Mon Sep 17 00:00:00 2001
From: DriesSchaumont <5946712+DriesSchaumont@users.noreply.github.com>
Date: Fri, 8 Nov 2024 09:26:23 +0000
Subject: [PATCH] Small updates

---
 CHANGELOG.md                                  |  2 --
 .../cellranger_mkref/config.vsh.yaml          | 29 ++++++++-----------
 src/cellranger/cellranger_mkref/script.sh     | 10 +++----
 src/cellranger/cellranger_mkref/test.sh       |  2 +-
 4 files changed, 18 insertions(+), 25 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 6206a5a1..3905de17 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -17,7 +17,6 @@
 * `rsem/rsem_calculate_expression`: Calculate expression levels (PR #93).
 
 * `cellranger`:
-  - `cellranger/cellranger_count`: Align fastq files using Cell Ranger count (PR #163).
   - `cellranger/cellranger_mkref`: Build a Cell Ranger-compatible reference folder from user-supplied genome FASTA and gene GTF files (PR #164).
 
 
@@ -30,7 +29,6 @@
 
 * `nanoplot`: Plotting tool for long read sequencing data and alignments (PR #95).
 
-
 ## BUG FIXES
 
 * `falco`: Fix a typo in the `--reverse_complement` argument (PR #157).
diff --git a/src/cellranger/cellranger_mkref/config.vsh.yaml b/src/cellranger/cellranger_mkref/config.vsh.yaml
index b0ee993f..b00c8f90 100644
--- a/src/cellranger/cellranger_mkref/config.vsh.yaml
+++ b/src/cellranger/cellranger_mkref/config.vsh.yaml
@@ -3,13 +3,15 @@ namespace: cellranger
 description: Build a Cell Ranger-compatible reference folder from user-supplied genome FASTA and gene GTF files.
 keywords: [ cellranger, single-cell, rna-seq, alignment, reference, gtf, fasta ]
 links:
-  documentation: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/advanced/references#header
+  documentation: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/advanced/references
   repository: https://github.com/10XGenomics/cellranger/blob/main/lib/python/cellranger/reference_builder.py
   homepage: https://www.10xgenomics.com/support/software/cell-ranger/latest
   issue_tracker: https://github.com/10XGenomics/cellranger/issues
 references:
   doi: 10.1038/ncomms14049
-license: Copyright (c) 2023 10x Genomics
+license: Proprietary
+requirements:
+  commands: [cellranger, pigz, unpigz, tar]
 authors:
   - __merge__: /src/_authors/emma_rousseau.yaml
     roles: [ author ]
@@ -27,6 +29,7 @@ arguments:
     example: transcriptome_annotation.gtf.gz
   - type: string
     name: "--reference_version"
+    required: false
     description: "Optional reference version string to include with reference"
   - type: file
     name: --output
@@ -44,24 +47,16 @@ test_resources:
 
 engines:
 - type: docker
-  image: quay.io/nf-core/cellranger:8.0.0
+  image: ghcr.io/data-intuitive/cellranger:8.0
   setup:
-    - type: docker
-      run: |
-        DEBIAN_FRONTEND=noninteractive apt update && \
-        apt upgrade -y && apt install -y procps pigz && rm -rf /var/lib/apt/lists/*
+    - type: apt
+      packages:
+        - procps
+        - pigz
   test_setup:
     - type: apt
-      packages: [ git, wget ]
-    - type: docker
-      run: |
-        TARGETARCH="${TARGETARCH:-$(dpkg --print-architecture)}" && \
-        TARGETOS="${TARGETOS:-linux}" && \
-        PATH="${PATH}:/usr/local/go/bin" && \
-        wget https://go.dev/dl/go1.21.4.$TARGETOS-$TARGETARCH.tar.gz && tar -C /usr/local/ -xzf go1.21.4.$TARGETOS-$TARGETARCH.tar.gz && \
-        rm go1.21.4.$TARGETOS-$TARGETARCH.tar.gz && \
-        git clone --branch v2.5.0 https://github.com/shenwei356/seqkit.git && \
-        cd seqkit/seqkit/ && go build && cp seqkit /usr/bin/ && cd ../../ && rm -rf seqkit && rm -r /usr/local/go
+      packages:
+        - seqkit
     - type: docker
       run: |
         cellranger --version | sed 's/ cellranger-/: /' > /var/software_versions.txt
diff --git a/src/cellranger/cellranger_mkref/script.sh b/src/cellranger/cellranger_mkref/script.sh
index 9ee4b25e..7179faae 100644
--- a/src/cellranger/cellranger_mkref/script.sh
+++ b/src/cellranger/cellranger_mkref/script.sh
@@ -3,19 +3,19 @@
 set -eo pipefail
 
 ## VIASH START
-par_genome_fasta="resources_test/test_data/reference_small.fa.gz"
-par_transcriptome_gtf="resources_test/test_data/reference_small.gtf.gz"
-par_output="gencode_v41_annotation_cellranger.tar.gz"
+par_genome_fasta="test_data/reference_small.fa.gz"
+par_transcriptome_gtf="test_data/reference_small.gtf.gz"
+par_output="output.tar.gz"
 ## VIASH END
 
 # create temporary directory
-tmpdir=$(mktemp -d "$VIASH_TEMP/$meta_name-XXXXXXXX")
+tmpdir=$(mktemp -d "$meta_temp_dir/$meta_name-XXXXXXXX")
 function clean_up {
     rm -rf "$tmpdir"
 }
 trap clean_up EXIT
 
-# just to make sure
+# We change into the tempdir later, so we need absolute paths.
 par_genome_fasta=$(realpath $par_genome_fasta)
 par_transcriptome_gtf=$(realpath $par_transcriptome_gtf)
 par_output=$(realpath $par_output)
diff --git a/src/cellranger/cellranger_mkref/test.sh b/src/cellranger/cellranger_mkref/test.sh
index 663c1c59..5c5c1f3d 100644
--- a/src/cellranger/cellranger_mkref/test.sh
+++ b/src/cellranger/cellranger_mkref/test.sh
@@ -3,7 +3,7 @@
 set -eou pipefail
 
 ## VIASH START
-meta_executable="bin/viash run src/reference/make_reference/config.vsh.yaml --"
+meta_executable="viash run src/reference/make_reference/config.vsh.yaml --"
 ## VIASH END
 
 # create temporary directory