Merge branch 'viash-hub:main' into main

CHANGELOG.md

@@ -4,6 +4,14 @@
 
 * `pear`: fix component not exiting with the correct exitcode when PEAR fails.
 
+* `cutadapt`: fix `--par_quality_cutoff_r2` argument.
+
+* `cutadapt`: demultiplexing is now disabled by default. It can be re-enabled by using `demultiplex_mode`.
+
+## MINOR CHANGES
+
+* `busco` components: update BUSCO to `5.7.1`.
+
 # biobox 0.1.0
 
 ## BREAKING CHANGES
@@ -12,6 +20,7 @@
   Viash 0.9.0 in order to avoid issues with the current default separator `:` unintentionally
   splitting up certain file paths.
 
+
 ## NEW FEATURES
 
 * `arriba`: Detect gene fusions from RNA-seq data (PR #1).

src/busco/busco_download_datasets/config.vsh.yaml

@@ -37,7 +37,7 @@ test_resources:
     path: test.sh
 engines:
   - type: docker
-    image: quay.io/biocontainers/busco:5.6.1--pyhdfd78af_0
+    image: quay.io/biocontainers/busco:5.7.1--pyhdfd78af_0
     setup:
       - type: docker
         run: |

src/busco/busco_list_datasets/config.vsh.yaml

@@ -29,7 +29,7 @@ test_resources:
     path: test.sh
 engines:
   - type: docker
-    image: quay.io/biocontainers/busco:5.6.1--pyhdfd78af_0
+    image: quay.io/biocontainers/busco:5.7.1--pyhdfd78af_0
     setup:
       - type: docker
         run: |

src/busco/busco_run/config.vsh.yaml

@@ -181,6 +181,10 @@ argument_groups:
 
   - name: MetaEuk Settings
     arguments:
+      - name: --metaeuk
+        type: boolean_true
+        description: |
+          Use Metaeuk gene predictor.
       - name: --metaeuk_parameters
         type: string
         description: |
@@ -204,7 +208,7 @@ test_resources:
     path: test_data
 engines:
   - type: docker
-    image: quay.io/biocontainers/busco:5.6.1--pyhdfd78af_0
+    image: quay.io/biocontainers/busco:5.7.1--pyhdfd78af_0
     setup:
       - type: docker
         run: |

src/busco/busco_run/help.txt

@@ -2,7 +2,9 @@
 busco -h
 ```
 
-Welcome to BUSCO 5.6.1: the Benchmarking Universal Single-Copy Ortholog assessment tool.
+usage: busco -i [SEQUENCE_FILE] -l [LINEAGE] -o [OUTPUT_NAME] -m [MODE] [OTHER OPTIONS]
+
+Welcome to BUSCO 5.7.1: the Benchmarking Universal Single-Copy Ortholog assessment tool.
 For more detailed usage information, please review the README file provided with this distribution and the BUSCO user guide. Visit this page https://gitlab.com/ezlab/busco#how-to-cite-busco to see how to cite BUSCO
 
 optional arguments:
@@ -18,7 +20,7 @@ optional arguments:
   -l LINEAGE, --lineage_dataset LINEAGE
                         Specify the name of the BUSCO lineage to be used.
   --augustus            Use augustus gene predictor for eukaryote runs
-  --augustus_parameters --PARAM1=VALUE1,--PARAM2=VALUE2
+  --augustus_parameters "--PARAM1=VALUE1,--PARAM2=VALUE2"
                         Pass additional arguments to Augustus. All arguments should be contained within a single string with no white space, with each argument separated by a comma.
   --augustus_species AUGUSTUS_SPECIES
                         Specify a species for Augustus training.
@@ -42,11 +44,12 @@ optional arguments:
   --limit N             How many candidate regions (contig or transcript) to consider per BUSCO (default: 3)
   --list-datasets       Print the list of available BUSCO datasets
   --long                Optimization Augustus self-training mode (Default: Off); adds considerably to the run time, but can improve results for some non-model organisms
+  --metaeuk             Use Metaeuk gene predictor
   --metaeuk_parameters "--PARAM1=VALUE1,--PARAM2=VALUE2"
                         Pass additional arguments to Metaeuk for the first run. All arguments should be contained within a single string with no white space, with each argument separated by a comma.
   --metaeuk_rerun_parameters "--PARAM1=VALUE1,--PARAM2=VALUE2"
                         Pass additional arguments to Metaeuk for the second run. All arguments should be contained within a single string with no white space, with each argument separated by a comma.
-  --miniprot            Use miniprot gene predictor
+  --miniprot            Use Miniprot gene predictor
   --skip_bbtools        Skip BBTools for assembly statistics
   --offline             To indicate that BUSCO cannot attempt to download files
   --opt-out-run-stats   Opt out of data collection. Information on the data collected is available in the user guide.

src/busco/busco_run/script.sh

@@ -39,6 +39,7 @@ busco \
     ${par_force:+--force} \
     ${par_limit:+--limit "$par_limit"} \
     ${par_long:+--long} \
+    ${par_metaeuk:+--metaeuk} \
     ${par_metaeuk_parameters:+--metaeuk_parameters "$par_metaeuk_parameters"} \
     ${par_metaeuk_rerun_parameters:+--metaeuk_rerun_parameters "$par_metaeuk_rerun_parameters"} \
     ${par_miniprot:+--miniprot} \

src/cutadapt/config.vsh.yaml

@@ -240,6 +240,24 @@ argument_groups:
           Check both the read and its reverse complement for adapter
           matches. If match is on reverse-complemented version,
           output that one.
+  
+  ####################################################################
+  - name: "Demultiplexing options"
+    arguments:
+      - name: "--demultiplex_mode"
+        type: string
+        choices: ["single", "unique_dual", "combinatorial_dual"]
+        required: false
+        description: |
+          Enable demultiplexing and set the mode for it.
+          With mode 'unique_dual', adapters from the first and second read are used,
+          and the indexes from the reads are only used in pairs. This implies
+          --pair_adapters.
+          Enabling mode 'combinatorial_dual' allows all combinations of the sets of indexes
+          on R1 and R2. It is necessary to write each read pair to an output
+          file depending on the adapters found on both R1 and R2.
+          Mode 'single', uses indexes or barcodes located at the 5'
+          end of the R1 read (single). 
 
   ####################################################################
   - name: Read modifications

src/cutadapt/script.sh

@@ -127,7 +127,7 @@ mod_args=$(echo \
   ${par_cut_r2:+--cut_r2 "${par_cut_r2}"} \
   ${par_nextseq_trim:+--nextseq-trim "${par_nextseq_trim}"} \
   ${par_quality_cutoff:+--quality-cutoff "${par_quality_cutoff}"} \
-  ${par_quality_cutoff_r2:+--quality-cutoff_r2 "${par_quality_cutoff_r2}"} \
+  ${par_quality_cutoff_r2:+-Q "${par_quality_cutoff_r2}"} \
   ${par_quality_base:+--quality-base "${par_quality_base}"} \
   ${par_poly_a:+--poly-a} \
   ${par_length:+--length "${par_length}"} \
@@ -196,14 +196,35 @@ else
   ext="fasta"
 fi
 
-if [ $mode = "se" ]; then
+demultiplex_mode="$par_demultiplex_mode"
+if [[ $mode == "se" ]]; then
+  if [[ "$demultiplex_mode" == "unique_dual" ]] || [[ "$demultiplex_mode" == "combinatorial_dual" ]]; then
+    echo "Demultiplexing dual indexes is not possible with single-end data."
+    exit 1
+  fi
+  prefix="trimmed_"
+  if [[ ! -z "$demultiplex_mode" ]]; then
+    prefix="{name}_"
+  fi
   output_args=$(echo \
-    --output "$output_dir/{name}_001.$ext" \
+    --output "$output_dir/${prefix}001.$ext" \
   )
 else
+  demultiplex_indicator_r1='{name}_'
+  demultiplex_indicator_r2=$demultiplex_indicator_r1
+  if [[ "$demultiplex_mode" == "combinatorial_dual" ]]; then
+    demultiplex_indicator_r1='{name1}_{name2}_'
+    demultiplex_indicator_r2='{name1}_{name2}_'
+  fi
+  prefix_r1="trimmed_"
+  prefix_r2="trimmed_"
+  if [[ ! -z "$demultiplex_mode" ]]; then
+    prefix_r1=$demultiplex_indicator_r1
+    prefix_r2=$demultiplex_indicator_r2
+  fi
   output_args=$(echo \
-    --output "$output_dir/{name}_R1_001.$ext" \
-    --paired-output "$output_dir/{name}_R2_001.$ext" \
+    --output "$output_dir/${prefix_r1}R1_001.$ext" \
+    --paired-output "$output_dir/${prefix_r2}R2_001.$ext" \
   )
 fi
 

src/cutadapt/test.sh

@@ -1,6 +1,7 @@
 #!/bin/bash
 
 set -e
+set -eo pipefail
 
 #############################################
 # helper functions
@@ -57,6 +58,7 @@ EOF
   --adapter ADAPTER \
   --input example.fa \
   --fasta \
+  --demultiplex_mode single \
   --no_match_adapter_wildcards \
   --json
 
@@ -101,6 +103,7 @@ EOF
   --output "out_test1/*.fasta" \
   --adapter ADAPTER \
   --input example.fa \
+  --demultiplex_mode single \
   --fasta \
   --no_match_adapter_wildcards \
   --json
@@ -160,6 +163,7 @@ EOF
   --adapter AAAAA \
   --adapter_fasta adapters1.fasta \
   --adapter_fasta adapters2.fasta \
+  --demultiplex_mode single \
   --input example.fa \
   --fasta \
   --json
@@ -224,6 +228,7 @@ EOF
   --input example_R1.fastq \
   --input_r2 example_R2.fastq \
   --quality_cutoff 20 \
+  --demultiplex_mode unique_dual \
   --json \
   ---cpus 1