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Fix bowtie1 regression (log). #39

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merged 1 commit into from
Dec 13, 2023
Merged

Fix bowtie1 regression (log). #39

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2 changes: 2 additions & 0 deletions README.rst
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Expand Up @@ -158,6 +158,8 @@ Changelog
========= ====================================================================
Version Description
========= ====================================================================
0.19.2 * fix bowtie1 regression in the log file
* set genome directory default to None to enforce its usage
0.19.1 * add rnaseqc container.
* Update rseqc rules (redirection)
* cleanup onsuccess rule
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2 changes: 1 addition & 1 deletion pyproject.toml
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Expand Up @@ -4,7 +4,7 @@ build-backend = "poetry.core.masonry.api"

[tool.poetry]
name = "sequana-rnaseq"
version = "0.19.1"
version = "0.19.2"
description = "A RNAseq pipeline from raw reads to feature counts"
authors = ["Sequana Team"]
license = "BSD-3"
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1 change: 0 additions & 1 deletion sequana_pipelines/rnaseq/main.py
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Expand Up @@ -60,7 +60,6 @@
@click.option(
"--genome-directory",
"genome_directory",
default=".",
show_default=True,
type=click.Path(dir_okay=True, file_okay=False),
required=True,
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4 changes: 2 additions & 2 deletions sequana_pipelines/rnaseq/rnaseq.rules
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Expand Up @@ -484,7 +484,7 @@ if manager.config.general.rRNA_feature or manager.config.general.contaminant_fil
input:
expand("{sample}/bowtie1_mapping_rna/{sample}_bowtie1.log", sample=manager.samples)
output:
"logs/fix_bowtie1_log"
"logs/fix_bowtie1/{sample}.log"
run:

for filename in input:
Expand All @@ -501,7 +501,7 @@ if manager.config.general.rRNA_feature or manager.config.general.contaminant_fil
fout.write(line)
with open(output[0], "w") as fout:
fout.write("")
expected_output += ["logs/fix_bowtie1_log"]
expected_output += expand("logs/fix_bowtie1/{sample}.log", sample=manager.samples)


# ========================================================== bowtie2 mapping
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