From e64ebdf8cf236a54cb82dafe851b7f33ed4cc1b2 Mon Sep 17 00:00:00 2001
From: emmarousseau <emmarou1@icloud.com>
Date: Wed, 18 Sep 2024 15:41:20 +0200
Subject: [PATCH] apply suggested changes (changelog, config)

---
 CHANGELOG.md                                | 15 +++++++--------
 src/kallisto/kallisto_quant/config.vsh.yaml |  6 ++++--
 2 files changed, 11 insertions(+), 10 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index a9ccf26b..b99fd09f 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -50,9 +50,14 @@
 
 * `fastqc`: High throughput sequence quality control analysis tool (PR #92).
 
+* `sortmerna`: Local sequence alignment tool for mapping, clustering, and filtering rRNA from
+  metatranscriptomic data (PR #146).
+
+* `fq_subsample`: Sample a subset of records from single or paired FASTQ files (PR #147).
+
 * `kallisto`:
-  - `kallisto/kallisto_quant`: Quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences  
-                               using high-throughput sequencing reads (PR #152).
+    - `kallisto_index`: Create a kallisto index (PR #149).
+    - `kallisto_quant`: Quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads (PR #152).
 
 
 ## MINOR CHANGES
@@ -151,13 +156,7 @@
     - `bedtools_getfasta`: extract sequences from a FASTA file for each of the
                            intervals defined in a BED/GFF/VCF file (PR #59).
 
-* `sortmerna`: Local sequence alignment tool for mapping, clustering, and filtering rRNA from metatranscriptomic 
-               data. (PR #146)
 
-* `fq_subsample`: Sample a subset of records from single or paired FASTQ files (PR #147).
-
-* `kallisto`:
-    - `kallisto_index`: Create a kallisto index (PR #149).
 
 
 ## MINOR CHANGES
diff --git a/src/kallisto/kallisto_quant/config.vsh.yaml b/src/kallisto/kallisto_quant/config.vsh.yaml
index 4fb7b0fe..e92ac6b3 100644
--- a/src/kallisto/kallisto_quant/config.vsh.yaml
+++ b/src/kallisto/kallisto_quant/config.vsh.yaml
@@ -9,7 +9,7 @@ links:
   repository: https://github.com/pachterlab/kallisto
   issue_tracker: https://github.com/pachterlab/kallisto/issues
 references: 
-  doi: https://doi.org/10.1038/nbt.3519
+  doi: 10.1038/nbt.3519
 license: BSD 2-Clause License
 
 argument_groups:
@@ -96,7 +96,9 @@ engines:
           apt-get install -y --no-install-recommends wget && \
           wget --no-check-certificate https://github.com/pachterlab/kallisto/releases/download/v0.50.1/kallisto_linux-v0.50.1.tar.gz && \
           tar -xzf kallisto_linux-v0.50.1.tar.gz && \
-          mv kallisto/kallisto /usr/local/bin/ && \
+          mv kallisto/kallisto /usr/local/bin/
+      - type: docker
+        run: |
           echo "kallisto: $(kallisto version | sed 's/kallisto, version //')" > /var/software_versions.txt
 runners:
   - type: executable