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Build branch main with version main (861319f)

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Build pipeline: vsh-ci-template-8vdc6

Source commit: 861319f5dd

Source message: Merge pull request #4 from viash-hub/update-star-align-params

update param
This commit is contained in:
CI
2025-02-03 16:59:21 +00:00
parent edccce830a
commit 5b1018434e
34 changed files with 5633 additions and 5991 deletions
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17
test_data.sh
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@@ -15,6 +15,11 @@ if [ ! -f "$TEST_DATA_DIR/SRR1570800_1.fastq" ] || [ ! -f "$TEST_DATA_DIR/SRR157
docker run -t --rm -v $PWD:/output:rw -w /output/test_data ncbi/sra-tools fasterq-dump -e 2 -p SRR1570800
fi
head -n 10000 "$TEST_DATA_DIR/SRR1569895_1.fastq" > "$TEST_DATA_DIR/SRR1569895_1_subsample.fastq"
head -n 10000 "$TEST_DATA_DIR/SRR1569895_2.fastq" > "$TEST_DATA_DIR/SRR1569895_2_subsample.fastq"
head -n 10000 "$TEST_DATA_DIR/SRR1570800_1.fastq" > "$TEST_DATA_DIR/SRR1570800_1_subsample.fastq"
head -n 10000 "$TEST_DATA_DIR/SRR1570800_2.fastq" > "$TEST_DATA_DIR/SRR1570800_2_subsample.fastq"
export NXF_SCM_FILE="$TEST_DATA_DIR/scm.config"
cat > $NXF_SCM_FILE << EOF
@@ -39,8 +44,8 @@ if [ ! -d "$TEST_DATA_DIR/S288C_reference_genome_Current_Release" ]; then
--publish_dir "$TEST_DATA_DIR"
fi
zcat "$TEST_DATA_DIR/S288C_reference_genome_Current_Release/S288C_reference_sequence_R64-5-1_20240529.fsa.gz" > "$TEST_DATA_DIR/S288C_reference_genome_Current_Release/S288C_reference_sequence_R64-5-1_20240529.fsa"
zcat "$TEST_DATA_DIR/S288C_reference_genome_Current_Release/saccharomyces_cerevisiae_R64-5-1_20240529.gff.gz" > "$TEST_DATA_DIR/S288C_reference_genome_Current_Release/saccharomyces_cerevisiae_R64-5-1_20240529.gff"
gunzip -c "$TEST_DATA_DIR/S288C_reference_genome_Current_Release/S288C_reference_sequence_R64-5-1_20240529.fsa.gz" > "$TEST_DATA_DIR/S288C_reference_genome_Current_Release/S288C_reference_sequence_R64-5-1_20240529.fsa"
gunzip -c "$TEST_DATA_DIR/S288C_reference_genome_Current_Release/saccharomyces_cerevisiae_R64-5-1_20240529.gff.gz" > "$TEST_DATA_DIR/S288C_reference_genome_Current_Release/saccharomyces_cerevisiae_R64-5-1_20240529.gff"
sed -i -e 's/^.*chromosome=\(.*\)\]$/>chr\1/' "$TEST_DATA_DIR/S288C_reference_genome_Current_Release/S288C_reference_sequence_R64-5-1_20240529.fsa"
if [ ! -d "$TEST_DATA_DIR/S288C_reference_genome_Current_Release_STAR" ]; then
@@ -59,11 +64,11 @@ PARAMS_FILE=params_file.yaml
cat > $PARAMS_FILE << EOF
param_list:
- id: SRR1569895
input_r1: $TEST_DATA_DIR/SRR1569895_1.fastq
input_r2: $TEST_DATA_DIR/SRR1569895_2.fastq
input_r1: $TEST_DATA_DIR/SRR1569895_1_subsample.fastq
input_r2: $TEST_DATA_DIR/SRR1569895_2_subsample.fastq
- id: SRR1570800
input_r1: $TEST_DATA_DIR/SRR1570800_1.fastq
input_r2: $TEST_DATA_DIR/SRR1570800_2.fastq
input_r1: $TEST_DATA_DIR/SRR1570800_1_subsample.fastq
input_r2: $TEST_DATA_DIR/SRR1570800_2_subsample.fastq
publish_dir: foo
reference: $TEST_DATA_DIR/S288C_reference_genome_Current_Release_STAR
EOF