From 4e7f7083f0b1cdc038374b59d970a9de833f394c Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Mon, 10 Oct 2022 12:29:18 +0200 Subject: [PATCH] test: Add --outdir --- tests/test_default.yml | 2 +- tests/test_hisat2.yml | 6 +++--- tests/test_salmon.yml | 4 ++-- tests/test_sra_download.yml | 2 +- tests/test_star_rsem.yml | 4 ++-- tests/test_star_salmon.yml | 24 ++++++++++++------------ 6 files changed, 21 insertions(+), 21 deletions(-) diff --git a/tests/test_default.yml b/tests/test_default.yml index 5aa4b708ca..4e324b4452 100644 --- a/tests/test_default.yml +++ b/tests/test_default.yml @@ -1,6 +1,6 @@ # NOTE For now these tests don't support any containers beside docker - name: Run default pipeline with test data - command: nextflow run main.nf -profile test,docker + command: nextflow run main.nf -profile test,docker --outdir results tags: - default files: diff --git a/tests/test_hisat2.yml b/tests/test_hisat2.yml index ac37e103e1..343d41fb27 100644 --- a/tests/test_hisat2.yml +++ b/tests/test_hisat2.yml @@ -1,12 +1,12 @@ # NOTE For now these tests don't support any containers beside docker - name: Test HISAT2 with skip_qc workflow parameters - command: nextflow run main.nf -profile test,docker --aligner hisat2 --skip_qc + command: nextflow run main.nf -profile test,docker --aligner hisat2 --skip_qc --outdir results tags: - hisat2 - skip_qc - name: Test HISAT2 with hisat2_index false workflow parameters - command: nextflow run main.nf -profile test,docker --aligner hisat2 --hisat2_index false + command: nextflow run main.nf -profile test,docker --aligner hisat2 --hisat2_index false --outdir results tags: - hisat2 - - "hisat2_index false" + - 'hisat2_index false' diff --git a/tests/test_salmon.yml b/tests/test_salmon.yml index 52481c344b..bfd2ae5c1d 100644 --- a/tests/test_salmon.yml +++ b/tests/test_salmon.yml @@ -1,6 +1,6 @@ # NOTE For now these tests don't support any containers beside docker - name: Test Salmon with skip_qc skip_alignment workflow parameters - command: nextflow run main.nf -profile test,docker --pseudo_aligner salmon --skip_qc --skip_alignment + command: nextflow run main.nf -profile test,docker --pseudo_aligner salmon --skip_qc --skip_alignment --outdir results tags: - salmon - skip_qc @@ -8,7 +8,7 @@ - "skip_qc skip_alignment" - name: Test Salmon with salmon_index false transcript_fasta false workflow parameters - command: nextflow run main.nf -profile test,docker --salmon_index false --transcript_fasta false + command: nextflow run main.nf -profile test,docker --salmon_index false --transcript_fasta false --outdir results tags: - salmon - salmon_index diff --git a/tests/test_sra_download.yml b/tests/test_sra_download.yml index cc6bd05efe..c31b7075c4 100644 --- a/tests/test_sra_download.yml +++ b/tests/test_sra_download.yml @@ -1,5 +1,5 @@ # NOTE For now these tests don't support any containers beside docker - name: Run pipeline to download public data - command: nextflow run main.nf -profile test_sra,docker + command: nextflow run main.nf -profile test_sra,docker --outdir results tags: - sra_download diff --git a/tests/test_star_rsem.yml b/tests/test_star_rsem.yml index c5f499f268..cb397de082 100644 --- a/tests/test_star_rsem.yml +++ b/tests/test_star_rsem.yml @@ -1,13 +1,13 @@ # NOTE For now these tests don't support any containers beside docker - name: Test STAR RSEM with skip_qc workflow parameters - command: nextflow run main.nf -profile test,docker --aligner star_rsem --skip_qc + command: nextflow run main.nf -profile test,docker --aligner star_rsem --skip_qc --outdir results tags: - star - rsem - skip_qc - name: Test STAR RSEM with rsem_index false workflow parameters - command: nextflow run main.nf -profile test,docker --aligner star_rsem --rsem_index false + command: nextflow run main.nf -profile test,docker --aligner star_rsem --rsem_index false --outdir results tags: - star - rsem diff --git a/tests/test_star_salmon.yml b/tests/test_star_salmon.yml index e040c2b099..6d244fbc80 100644 --- a/tests/test_star_salmon.yml +++ b/tests/test_star_salmon.yml @@ -1,13 +1,13 @@ # NOTE For now these tests don't support any containers beside docker - name: Test STAR Salmon with skip_qc workflow parameters - command: nextflow run main.nf -profile test,docker --aligner star_salmon --skip_qc + command: nextflow run main.nf -profile test,docker --aligner star_salmon --skip_qc --outdir results tags: - star - salmon - skip_qc - name: Test STAR Salmon with remove_ribo_rna workflow parameters - command: nextflow run main.nf -profile test,docker --aligner star_salmon --remove_ribo_rna + command: nextflow run main.nf -profile test,docker --aligner star_salmon --remove_ribo_rna --outdir results tags: - star - salmon @@ -16,49 +16,49 @@ exit_code: 1 - name: Test STAR Salmon with skim_trimming workflow parameters - command: nextflow run main.nf -profile test,docker --aligner star_salmon --skim_trimming + command: nextflow run main.nf -profile test,docker --aligner star_salmon --skim_trimming --outdir results tags: - star - salmon - skim_trimming - name: Test STAR Salmon with gtf false workflow parameters - command: nextflow run main.nf -profile test,docker --aligner star_salmon --gtf false + command: nextflow run main.nf -profile test,docker --aligner star_salmon --gtf false --outdir results tags: - star - salmon - "gtf false" - name: Test STAR Salmon with star_index false workflow parameters - command: nextflow run main.nf -profile test,docker --aligner star_salmon --star_index false + command: nextflow run main.nf -profile test,docker --aligner star_salmon --star_index false --outdir results tags: - star - salmon - "star_index false" - name: Test STAR Salmon with transcript_fasta false workflow parameters - command: nextflow run main.nf -profile test,docker --aligner star_salmon --transcript_fasta false + command: nextflow run main.nf -profile test,docker --aligner star_salmon --transcript_fasta false --outdir results tags: - star - salmon - "transcript_fasta" - name: Test STAR Salmon with min_mapped_reads 90 workflow parameters - command: nextflow run main.nf -profile test,docker --aligner star_salmon --min_mapped_reads 90 + command: nextflow run main.nf -profile test,docker --aligner star_salmon --min_mapped_reads 90 --outdir results tags: - star - salmon - "min_mapped_reads 90" - name: Test STAR Salmon with with_umi workflow parameters - command: nextflow run main.nf -profile test,docker --aligner star_salmon --with_umi + command: nextflow run main.nf -profile test,docker --aligner star_salmon --with_umi --outdir results tags: - star - salmon - with_umi - name: Test STAR Salmon with with_umi skip_trimming workflow parameters - command: nextflow run main.nf -profile test,docker --aligner star_salmon --with_umi --skip_trimming + command: nextflow run main.nf -profile test,docker --aligner star_salmon --with_umi --skip_trimming --outdir results tags: - star - salmon @@ -66,21 +66,21 @@ - skip_trimming - name: Test STAR Salmon with bam_csi_index workflow parameters - command: nextflow run main.nf -profile test,docker --aligner star_salmon --bam_csi_index + command: nextflow run main.nf -profile test,docker --aligner star_salmon --bam_csi_index --outdir results tags: - star - salmon - "bam_csi_index" - name: Test STAR Salmon with save_align_intermeds save_reference workflow parameters - command: nextflow run main.nf -profile test,docker --aligner star_salmon --save_align_intermeds --save_reference + command: nextflow run main.nf -profile test,docker --aligner star_salmon --save_align_intermeds --save_reference --outdir results tags: - star - salmon - "save_reference" - name: Test STAR Salmon with featurecounts_group_type false workflow parameters - command: nextflow run main.nf -profile test,docker --aligner star_salmon --featurecounts_group_type false + command: nextflow run main.nf -profile test,docker --aligner star_salmon --featurecounts_group_type false --outdir results tags: - star - salmon