functional tests, changelog, remove defaults from config

CHANGELOG.md

@@ -131,6 +131,8 @@
     - `bedtools_getfasta`: extract sequences from a FASTA file for each of the
                            intervals defined in a BED/GFF/VCF file (PR #59).
 
+*  `fq_subsample`: Sample a subset of records from single or paired FASTQ files (PR #147).
+
 ## MINOR CHANGES
 
 * Uniformize component metadata (PR #23).

src/fq_subsample/config.vsh.yaml

@@ -23,12 +23,10 @@ argument_groups:
   - name: "--output_1"
     type: file
     direction: output
-    default: $id.read_1.subsampled.fastq
     description: Sampled read 1 fastq files. Output will be gzipped if ends in `.gz`.
   - name: "--output_2"
     type: file
     direction: output
-    default: $id.read_2.subsampled.fastq
     description: Sampled read 2 fastq files. Output will be gzipped if ends in `.gz`.
 
 - name: "Options"
@@ -58,14 +56,14 @@ engines:
     setup: 
       - type: docker
         env: 
-            - TZ Europe/Brussels
+            - TZ=Europe/Brussels
         run: | 
           ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone && \
           apt-get update && \
           apt-get install -y --no-install-recommends build-essential git-all curl && \
           curl https://sh.rustup.rs -sSf | sh -s -- -y && \
           . "$HOME/.cargo/env" && \
-          git clone --depth 1 --branch v0.11.0 https://github.com/stjude-rust-labs/fq.git && \
+          git clone --depth 1 --branch v0.12.0 https://github.com/stjude-rust-labs/fq.git && \
           mv fq /usr/local/ && cd /usr/local/fq && \
           cargo install --locked --path . && \
           mv /usr/local/fq/target/release/fq /usr/local/bin/

src/fq_subsample/test.sh

@@ -4,32 +4,32 @@ echo ">>> Testing $meta_executable"
 
 echo ">>> Testing for paired-end reads"
 "$meta_executable" \
-    --input_1 $meta_resources_dir/test_data/a.1.fastq \
-    --input_2 $meta_resources_dir/test_data/a.1.fastq \
+    --input_1 $meta_resources_dir/test_data/a.3.fastq.gz \
+    --input_2 $meta_resources_dir/test_data/a.4.fastq.gz \
     --record_count 3 \
     --seed 1 \
     --output_1  a.1.subsampled.fastq \
     --output_2  a.2.subsampled.fastq 
 
 echo ">> Checking if the correct files are present"
 [ ! -f "a.1.subsampled.fastq" ] && echo "Subsampled FASTQ file for read 1 is missing!" && exit 1
-[ ! -s "a.1.subsampled.fastq" ] && echo "Subsampled FASTQ file is empty!" && exit 1
+[ $(wc -l < a.1.subsampled.fastq) -ne 12 ] && echo "Subsampled FASTQ file for read 1 does not contain the expected number of records" && exit 1
 [ ! -f "a.2.subsampled.fastq" ] && echo "Subsampled FASTQ file for read 2 is missing" && exit 1
-[ ! -s "a.2.subsampled.fastq" ] && echo "Subsampled FASTQ file is empty" && exit 1
+[ $(wc -l < a.2.subsampled.fastq) -ne 12 ] && echo "Subsampled FASTQ file for read 2 does not contain the expected number of records" && exit 1
 
 rm a.1.subsampled.fastq a.2.subsampled.fastq
 
 echo ">>> Testing for single-end reads"
 "$meta_executable" \
-    --input_1 $meta_resources_dir/test_data/a.1.fastq \
-    --input_2 $meta_resources_dir/test_data/a.1.fastq \
+    --input_1 $meta_resources_dir/test_data/a.3.fastq.gz \
     --record_count 3 \
     --seed 1 \
     --output_1  a.1.subsampled.fastq 
+
 
 echo ">> Checking if the correct files are present"
 [ ! -f "a.1.subsampled.fastq" ] && echo "Subsampled FASTQ file is missing" && exit 1
-[ ! -s "a.1.subsampled.fastq" ] && echo "Subsampled FASTQ file is empty" && exit 1
+[ $(wc -l < a.1.subsampled.fastq) -ne 12 ] && echo "Subsampled FASTQ file does not contain the expected number of records" && exit 1
 
 echo ">>> Tests finished successfully"
 exit 0