Merge remote-tracking branch 'origin/main' into add_lofreq

CHANGELOG.md

@@ -8,7 +8,10 @@
 
 * `fastp`: An ultra-fast all-in-one FASTQ preprocessor (PR #3).
 
-* `busco`: Assess genome assembly and annotation completeness with single copy orthologs (PR #6).
+* `busco`: 
+    - `busco/busco_run`: Assess genome assembly and annotation completeness with single copy orthologs (PR #6).
+    - `busco/busco_list_datasets`: Lists available busco datasets (PR #18).
+    - `busco/busco_download_datasets`: Download busco datasets (PR #19).
 
 * `featurecounts`: Assign sequence reads to genomic features (PR #11).
 
@@ -24,6 +27,8 @@
 
 ## MINOR CHANGES
 
+* Uniformize component metadata (PR #23).
+
 ## DOCUMENTATION
 
 ## BUG FIXES

src/arriba/config.vsh.yaml

@@ -3,11 +3,13 @@ functionality:
   description: Detect gene fusions from RNA-Seq data
   info:
     keywords: [Gene fusion, RNA-Seq]
-    homepage: https://arriba.readthedocs.io/en/latest/
-    documentation: https://arriba.readthedocs.io/en/latest/
-    repository: https://github.com/suhrig/arriba
-    reference: "doi:10.1101/gr.257246.119"
-    licence: MIT
+    links:
+      homepage: https://arriba.readthedocs.io/en/latest/
+      documentation: https://arriba.readthedocs.io/en/latest/
+      repository: https://github.com/suhrig/arriba
+    references:
+      doi: 10.1101/gr.257246.119
+    license: MIT
   requirements:
     cpus: 1
     commands: [ arriba ]

src/bgzip/config.vsh.yaml

@@ -2,12 +2,13 @@ functionality:
   name: bgzip
   description: Block compression/decompression utility
   info:
-    homepage: https://www.htslib.org/
-    documentation: https://www.htslib.org/doc/bgzip.html
-    repository: https://github.com/samtools/htslib
-    licence: MIT
-    reference:
+    links:
+      homepage: https://www.htslib.org/
+      documentation: https://www.htslib.org/doc/bgzip.html
+      repository: https://github.com/samtools/htslib
+    references:
       doi: 10.1093/gigascience/giab007
+    license: MIT
   requirements:
     commands: [ bgzip ]
   argument_groups:

src/busco/busco_download_datasets/config.vsh.yaml

@@ -0,0 +1,46 @@
+functionality:
+  name: busco_download_datasets
+  namespace: busco
+  description: Downloads available busco datasets
+  info:
+    links:
+      homepage: https://busco.ezlab.org/
+      documentation: https://busco.ezlab.org/busco_userguide.html
+      repository: https://gitlab.com/ezlab/busco
+    references:
+      doi: 10.1007/978-1-4939-9173-0_14
+    license: MIT
+  argument_groups:
+    - name: Inputs
+      arguments:
+        - name: --download
+          type: string
+          description: |
+            Download dataset. Possible values are a specific dataset name, "all", "prokaryota", "eukaryota", or "virus".
+            The full list of available datasets can be viewed [here](https://busco-data.ezlab.org/v5/data/lineages/) or by running the busco/busco_list_datasets component.
+          required: true
+          example: stramenopiles_odb10
+    - name: Outputs
+      arguments:
+        - name: --download_path
+          direction: output
+          type: file
+          description: |
+            Local filepath for storing BUSCO dataset downloads
+          required: false
+          default: busco_downloads
+          example: busco_downloads
+  resources:
+    - type: bash_script
+      path: script.sh
+  test_resources:
+    - type: bash_script
+      path: test.sh
+platforms:
+  - type: docker
+    image: quay.io/biocontainers/busco:5.6.1--pyhdfd78af_0
+    setup:
+      - type: docker
+        run: |
+          busco --version | sed 's/BUSCO\s\(.*\)/busco: "\1"/' > /var/software_versions.txt
+  - type: nextflow

src/busco/busco_download_datasets/script.sh

@@ -0,0 +1,14 @@
+#!/bin/bash
+
+## VIASH START
+## VIASH END
+
+
+if [ ! -d "$par_download_path" ]; then
+    mkdir -p "$par_download_path"
+fi
+
+busco \
+    --download_path "$par_download_path" \
+    --download "$par_download"
+

src/busco/busco_download_datasets/test.sh

@@ -0,0 +1,15 @@
+echo "> Downloading busco stramenopiles_odb10 dataset"
+
+"$meta_executable" \
+    --download stramenopiles_odb10 \
+    --download_path downloads 
+
+echo ">> Checking output"
+[ ! -f "downloads/file_versions.tsv" ] && echo "file_versions.tsv does not exist" && exit 1
+[ ! -f "downloads/lineages/stramenopiles_odb10/dataset.cfg" ] && echo "dataset.cfg does not exist" && exit 1
+
+echo ">> Checking if output is empty"
+[ ! -s "downloads/file_versions.tsv" ] && echo "file_versions.tsv is empty" && exit 1
+[ ! -s "downloads/lineages/stramenopiles_odb10/dataset.cfg" ] && echo "dataset.cfg is empty" && exit 1
+
+rm -r downloads

src/busco/busco_list_datasets/config.vsh.yaml

@@ -0,0 +1,38 @@
+functionality:
+  name: busco_list_datasets
+  namespace: busco
+  description: Lists the available busco datasets
+  info:
+    links:
+      homepage: https://busco.ezlab.org/
+      documentation: https://busco.ezlab.org/busco_userguide.html
+      repository: https://gitlab.com/ezlab/busco
+    references:
+      doi: 10.1007/978-1-4939-9173-0_14
+    license: MIT
+  argument_groups:
+    - name: Outputs
+      arguments:
+        - name: --output
+          alternatives: ["-o"]
+          direction: output
+          type: file
+          description: |
+            Output file of the available busco datasets
+          required: false
+          default: busco_dataset_list.txt
+          example: file.txt
+  resources:
+    - type: bash_script
+      path: script.sh
+  test_resources:
+    - type: bash_script
+      path: test.sh
+platforms:
+  - type: docker
+    image: quay.io/biocontainers/busco:5.6.1--pyhdfd78af_0
+    setup:
+      - type: docker
+        run: |
+          busco --version | sed 's/BUSCO\s\(.*\)/busco: "\1"/' > /var/software_versions.txt
+  - type: nextflow

src/busco/busco_list_datasets/script.sh

@@ -0,0 +1,6 @@
+#!/bin/bash
+
+## VIASH START
+## VIASH END
+
+busco --list-datasets | awk '/^#{40}/{flag=1; next} flag{print}' > $par_output

src/busco/busco_list_datasets/test.sh

@@ -0,0 +1,15 @@
+#!/bin/bash
+
+## VIASH START
+## VIASH END
+
+"$meta_executable" \
+    --output datasets.txt 
+
+echo ">> Checking output"
+[ ! -f "datasets.txt" ] && echo "datasets.txt does not exist" && exit 1
+
+echo ">> Checking if output is empty"
+[ ! -s "datasets.txt" ] && echo "datasets.txt is empty" && exit 1
+
+rm datasets.txt

src/busco/config.vsh.yaml → src/busco/busco_run/config.vsh.yaml

@@ -1,13 +1,16 @@
 functionality:
-  name: busco
+  name: busco_run
+  namespace: busco
   description: Assessment of genome assembly and annotation completeness with single copy orthologs
   info:
     keywords: [Genome assembly, quality control]
-    homepage: https://busco.ezlab.org/
-    documentation: https://busco.ezlab.org/busco_userguide.html
-    repository: https://gitlab.com/ezlab/busco
-    reference: "10.1007/978-1-4939-9173-0_14"
-    licence: MIT
+    links:
+      homepage: https://busco.ezlab.org/
+      documentation: https://busco.ezlab.org/busco_userguide.html
+      repository: https://gitlab.com/ezlab/busco
+    references:
+      doi: 10.1007/978-1-4939-9173-0_14
+    license: MIT
   argument_groups:
     - name: Inputs
       arguments:
@@ -35,9 +38,11 @@ functionality:
           required: false
           description: |
             Specify a BUSCO lineage dataset that is most closely related to the assembly or gene set being assessed. 
-            The full list of available datasets can be viewed [here](https://busco-data.ezlab.org/v5/data/lineages/) or by running `busco --list-datasets` (which requires installing the tool).
+            The full list of available datasets can be viewed [here](https://busco-data.ezlab.org/v5/data/lineages/) or by running the busco/busco_list_datasets component.
             When unsure, the "--auto_lineage" flag can be set to automatically find the optimal lineage path.
-            Requested datasets will automatically be downloaded if not already present in the download folder.
+            BUSCO will automatically download the requested dataset if it is not already present in the download folder. 
+            You can optionally provide a path to a local dataset instead of a name, e.g. path/to/dataset.
+            Datasets can be downloaded using the busco/busco_download_dataset component.
           example: stramenopiles_odb10
 
     - name: Outputs

src/fastp/config.vsh.yaml

@@ -22,10 +22,12 @@ functionality:
       - support ultra-fast FASTQ-level deduplication
   info:
     keywords: [RNA-Seq, Trimming, Quality control]
-    repository: https://github.com/OpenGene/fastp
-    documentation: https://github.com/OpenGene/fastp/blob/master/README.md
-    reference: "doi:10.1093/bioinformatics/bty560"
-    licence: MIT
+    links:
+      repository: https://github.com/OpenGene/fastp
+      documentation: https://github.com/OpenGene/fastp/blob/master/README.md
+    references:
+      doi: 10.1093/bioinformatics/bty560
+    license: MIT
   argument_groups:
     - name: Inputs
       description: |

src/featurecounts/config.vsh.yaml

@@ -4,11 +4,13 @@ functionality:
     featureCounts is a read summarization program for counting reads generated from either RNA or genomic DNA sequencing experiments by implementing highly efficient chromosome hashing and feature blocking techniques. It works with either single or paired-end reads and provides a wide range of options appropriate for different sequencing applications.
   info:
     keywords: ["Read counting", "Genomic features"]
-    homepage: https://subread.sourceforge.net/
-    documentation: https://subread.sourceforge.net/SubreadUsersGuide.pdf
-    repository: https://github.com/ShiLab-Bioinformatics/subread
-    reference: "doi:10.1093/bioinformatics/btt656"
-    licence: GPL-3.0 
+    links:
+      homepage: https://subread.sourceforge.net/
+      documentation: https://subread.sourceforge.net/SubreadUsersGuide.pdf
+      repository: https://github.com/ShiLab-Bioinformatics/subread
+    references:
+      doi: 10.1093/bioinformatics/btt656
+    license: GPL-3.0 
   requirements:
     commands: [ featureCounts ]
 

src/pear/config.vsh.yaml

@@ -6,11 +6,13 @@ functionality:
     PEAR evaluates all possible paired-end read overlaps and without requiring the target fragment size as input. In addition, it implements a statistical test for minimizing false-positive results. Together with a highly optimized implementation, it can merge millions of paired end reads within a couple of minutes on a standard desktop computer.
   info:
     keywords: [ "pair-end", "read", "merge" ]
-    homepage: https://cme.h-its.org/exelixis/web/software/pear
-    repository: https://github.com/tseemann/PEAR
-    documentation: https://cme.h-its.org/exelixis/web/software/pear/doc.html
-    reference: doi:10.1093/bioinformatics/btt593
-    licence: "CC-BY-NC-SA-3.0"
+    links:
+      homepage: https://cme.h-its.org/exelixis/web/software/pear
+      repository: https://github.com/tseemann/PEAR
+      documentation: https://cme.h-its.org/exelixis/web/software/pear/doc.html
+    references:
+      doi: 10.1093/bioinformatics/btt593
+    license: "CC-BY-NC-SA-3.0"
   requirements:
     commands: [ pear , gzip ]
   argument_groups: