reorganized seqtk namespace + added seqtk subseq config and script

viash-hub · Jul 5, 2024 · 51c69e9 · 51c69e9
1 parent 796c3bc
commit 51c69e9
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Showing 12 changed files with 83 additions and 5 deletions.
diff --git a/src/seqtk/seqtk_sample/config.vsh.yaml b/src/seqtk/seqtk_sample/config.vsh.yaml
@@ -44,7 +44,7 @@ test_resources:
   - type: bash_script
     path: test.sh
   - type: file
-    path: test_data
+    path: ../test_data
 
 engines:
   - type: docker

diff --git a/src/seqtk/seqtk_sample/script.sh b/src/seqtk/seqtk_sample/script.sh
@@ -4,7 +4,7 @@
 ## VIASH END
 
 seqtk sample \
-    ${par_2_pass_mode:+-2} \
+    ${par_two_pass_mode:+-2} \
     ${par_seed:+-s "$par_seed"} \
     "$par_input" \
     "$par_fraction_number" \

diff --git a/src/seqtk/seqtk_sample/test.sh b/src/seqtk/seqtk_sample/test.sh
@@ -4,7 +4,7 @@ set -e
 
 ## VIASH START
 meta_executable="target/executable/seqtk/seqtk_sample"
-meta_resources_dir="src/seqtk/seqtk_sample"
+meta_resources_dir="src/seqtk"
 ## VIASH END
 
 #########################################################################################

diff --git a/src/seqtk/seqtk_subseq/config.vsh.yaml b/src/seqtk/seqtk_subseq/config.vsh.yaml
@@ -0,0 +1,60 @@
+name: seqtk_subseq
+namespace: seqtk
+description: 
+keywords: [tag1, tag2]
+links:
+  repository: https://github.com/lh3/seqtk/tree/v1.4
+license: MIT
+
+argument_groups:
+  - name: Inputs
+    arguments:
+      - name: --input
+        type: file
+        description: The input FASTA/Q file.
+        required: true
+      - name: "--regions_file"
+        type: file
+        description: |
+          File with regions to extract. Can be either a list file 
+          with one sequence name per line or a bed file.
+        required: true
+
+  - name: Outputs
+    arguments:
+      - name: --output
+        type: file
+        description: The output FASTA/Q file.
+        required: true
+        direction: output
+
+  - name: Options
+    arguments:
+      - name: "--tab"
+        type: boolean
+        description: Output in tab-delimited format.
+        default: false
+      - name: "--strand_aware"
+        type: boolean
+        description: Strand-aware mode.
+        default: false
+      - name: "--line_length"
+        type: integer
+        description: Number of bases per line.
+        default: 60
+
+resources:
+  - type: bash_script
+    path: script.sh
+test_resources:
+  - type: bash_script
+    path: test.sh
+  - type: file
+    path: ../test_data
+
+engines:
+  - type: docker
+    image: quay.io/biocontainers/seqtk:1.4--he4a0461_2
+runners:
+  - type: executable
+  - type: nextflow
diff --git a/src/seqtk/seqtk_subseq/help.txt b/src/seqtk/seqtk_subseq/help.txt
@@ -0,0 +1,7 @@
+```
+seqtk_sample
+```
+Usage:   seqtk sample [-2] [-s seed=11] <in.fa> <frac>|<number> > <out.fa>
+
+Options: -s INT       RNG seed [11]
+         -2           2-pass mode: twice as slow but with much reduced memory
diff --git a/src/seqtk/seqtk_subseq/script.sh b/src/seqtk/seqtk_subseq/script.sh
@@ -0,0 +1,11 @@
+#!/bin/bash
+
+## VIASH START
+## VIASH END
+
+seqtk sample \
+    ${par_tab:+-t} \
+    ${par_strand_aware:+-s} \
+    ${par_line_length:+-l "$par_line_length"} \
+    "$par_input" \
+    > "$par_output"
diff --git a/...seqtk_sample/test_data/reads/a.1.fastq.gz → src/seqtk/test_data/reads/a.1.fastq.gz b/...seqtk_sample/test_data/reads/a.1.fastq.gz → src/seqtk/test_data/reads/a.1.fastq.gz
diff --git a/...seqtk_sample/test_data/reads/a.2.fastq.gz → src/seqtk/test_data/reads/a.2.fastq.gz b/...seqtk_sample/test_data/reads/a.2.fastq.gz → src/seqtk/test_data/reads/a.2.fastq.gz
diff --git a/...eqtk/seqtk_sample/test_data/reads/a.fastq → src/seqtk/test_data/reads/a.fastq b/...eqtk/seqtk_sample/test_data/reads/a.fastq → src/seqtk/test_data/reads/a.fastq
diff --git a/...k/seqtk_sample/test_data/reads/a.fastq.gz → src/seqtk/test_data/reads/a.fastq.gz b/...k/seqtk_sample/test_data/reads/a.fastq.gz → src/seqtk/test_data/reads/a.fastq.gz
diff --git a/...eqtk/seqtk_sample/test_data/reads/id.list → src/seqtk/test_data/reads/id.list b/...eqtk/seqtk_sample/test_data/reads/id.list → src/seqtk/test_data/reads/id.list
diff --git a/src/seqtk/seqtk_sample/test_data/script.sh → src/seqtk/test_data/script.sh b/src/seqtk/seqtk_sample/test_data/script.sh → src/seqtk/test_data/script.sh
@@ -4,6 +4,6 @@ if [ ! -d /tmp/snakemake-wrappers ]; then
 fi
 
 # copy test data
-cp -r /tmp/snakemake-wrappers/bio/seqtk/test/* src/seqtk/seqtk_sample/test_data
+cp -r /tmp/snakemake-wrappers/bio/seqtk/test/* src/seqtk/test_data
 
-rm src/seqtk/seqtk_sample/test_data/Snakefile
+rm src/seqtk/test_data/Snakefile