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Merge branch 'master' into fix-add-library-complexity
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CChahrour authored Mar 26, 2024

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2 parents e2d0506 + 23d5210 commit 50a415e
Showing 3 changed files with 6 additions and 5 deletions.
2 changes: 1 addition & 1 deletion seqnado/workflow/config/config.yaml.jinja
Original file line number Diff line number Diff line change
@@ -16,7 +16,7 @@ genome:

fastq_screen: "{{fastq_screen}}"
fastq_screen_config: "{{fastq_screen_config}}"

library_complexity: "{{library_complexity}}"
remove_blacklist: "{{remove_blacklist}}"
blacklist: "{{blacklist}}"

2 changes: 1 addition & 1 deletion seqnado/workflow/rules/exogenous_norm.smk
Original file line number Diff line number Diff line change
@@ -4,8 +4,8 @@ NORM_GROUPS = NormGroups.from_design(DESIGN)

use rule align_paired as align_paired_spikein with:
params:
index=config["genome"]["indices"],
options="--no-mixed --no-discordant",
index=config["genome"]["indices"],
output:
bam=temp("seqnado_output/aligned/spikein/raw/{sample}.bam"),
resources:
7 changes: 4 additions & 3 deletions tests/test_pipelines.py
Original file line number Diff line number Diff line change
@@ -62,8 +62,8 @@ def genome_indices_path(genome_path, assay) -> pathlib.Path:
return genome_path / "STAR_chr21_rna_spikein"


@pytest.fixture(scope="function", autouse=True)
def indicies(genome_indices_path, genome_path):
@pytest.fixture(scope="function")
def indicies(genome_indices_path, genome_path) -> pathlib.Path:

download_indices = True if not genome_indices_path.exists() else False
suffix = genome_indices_path.with_suffix(".tar.gz").name
@@ -195,11 +195,12 @@ def user_inputs(test_data_path, indicies, chromsizes, assay, assay_type, gtf, bl
defaults = {
"project_name": "test",
"genome_name": "hg38",
"indices": indicies,
"indices": str(indicies),
"chromsizes": str(chromsizes),
"gtf": str(gtf),
"blacklist": str(blacklist),
"fastq_screen": "no",
"library_complexity": "yes",
"remove_blacklist": "yes",
}

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