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Commit 556f1e12 authored by Alex Kanitz's avatar Alex Kanitz
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Refactor LabKey to Snakemake script

- clean up command line interface
  - improve descriptions
  - add consistent structure
  - remove or merge superfluous CLI arguments
  - set defaults
  - update test calls
  - update docs
  - when importing data from LabKey, table is saved to 'samples.tsv.labkey' in same directory as Snakemake sample table
- allow user to specify environment variables and relative paths in input table and on CLI
  - relative paths in the input table are interpreted with respect to the directory containing the input table
  - relative paths will are interpreted with respect to the current working directory; this is to achieve portability with respect to tests but is discouraged in production because its behavior is not very predictable from the user's perspective; consequently a warning is thrown
- set STAR index size to read length - 1
- remove `gtf_filtered` and `tr_fasta_filtered` and update Snakefiles and test sample tables accordingly
- rename some MultiQC report-related parameters and update Snakefiles and test config files accordingly
- add logging
- add docstrings to module and all functions
- add typing definitions to all functions
- restructure and comment code to improve readability
- linters `flake8` and `mypy` pass
parent 6cf28511
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1 merge request!62Major refactoring before release
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......@@ -243,9 +243,9 @@ you do not have these):
```bash
cat << EOF | ( umask 0377; cat >> ${HOME}/.netrc; )
machine <remote-instance-of-labkey-server>
machine <remote-instance-of-labkey-server>
login <user-email>
password <user-password>
password <user-password>
EOF
```
......@@ -255,13 +255,13 @@ help screen with option '--help' for further options and information):
```bash
python scripts/labkey_to_snakemake.py \
--input_dict="scripts/labkey_to_snakemake.dict.tsv" \
--labkey-domain="my.labkey.service.io"
--labkey-domain="/my/project/path"
--input-to-output-mapping="scripts/labkey_to_snakemake.dict.tsv" \
--resources-dir="/path/to/my/genome/resources" \
--output-table="config/my_run/samples.tsv" \
--config_file="config/my_run/config.yaml" \
--samples_table="config/my_run/samples.tsv" \
--remote \
--project-name="project_name" \
--table-name="table_name" \
<path_to_annotation_files>
<table_name>
```
#### Additional information
......
......@@ -1121,9 +1121,9 @@ rule prepare_multiqc_config:
"multiqc_config.yaml")
params:
logo_path = config['logo'],
multiqc_intro_text = config['multiqc_intro_text'],
url = config['multiqc_url']
logo_path = config['report_logo'],
multiqc_intro_text = config['report_description'],
url = config['report_url']
log:
stderr = os.path.join(
......
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......@@ -6,7 +6,7 @@
salmon_indexes: "results/salmon_indexes"
star_indexes: "results/star_indexes"
alfa_indexes: "results/alfa_indexes"
logo: "../../images/logo.128px.png"
multiqc_intro_text: "No description provided by user"
multiqc_url: "https://zavolan.biozentrum.unibas.ch/"
report_description: "No description provided by user"
report_logo: "../../images/logo.128px.png"
report_url: "https://zavolan.biozentrum.unibas.ch/"
...
\ No newline at end of file
......@@ -6,7 +6,7 @@
salmon_indexes: "results/salmon_indexes/"
star_indexes: "results/star_indexes/"
alfa_indexes: "results/alfa_indexes/"
logo: "../../images/logo.128px.png"
multiqc_intro_text: "No description provided by user"
multiqc_url: "https://zavolan.biozentrum.unibas.ch/"
report_description: "No description provided by user"
report_logo: "../../images/logo.128px.png"
report_url: "https://zavolan.biozentrum.unibas.ch/"
...
sample seqmode fq1 index_size kmer fq1_3p fq1_5p organism gtf gtf_filtered genome tr_fasta_filtered sd mean multimappers soft_clip pass_mode libtype fq1_polya_3p fq1_polya_5p kallisto_directionality alfa_directionality alfa_plus alfa_minus fq2 fq2_3p fq2_5p fq2_polya_3p fq2_polya_5p
synthetic_10_reads_paired_synthetic_10_reads_paired pe ../input_files/project1/synthetic.mate_1.fastq.gz 75 31 AGATCGGAAGAGCACA XXXXXXXXXXXXX homo_sapiens ../input_files/homo_sapiens/annotation.gtf ../input_files/homo_sapiens/annotation.gtf ../input_files/homo_sapiens/genome.fa ../input_files/homo_sapiens/transcriptome.fa 100 250 10 EndToEnd None A AAAAAAAAAAAAAAAAA XXXXXXXXXXXXXXXXX --fr fr-firststrand str1 str2 ../input_files/project1/synthetic.mate_2.fastq.gz AGATCGGAAGAGCGT XXXXXXXXXXXXX XXXXXXXXXXXXXXXXX TTTTTTTTTTTTTTTTT
synthetic_10_reads_mate_1_synthetic_10_reads_mate_1 se ../input_files/project2/synthetic.mate_1.fastq.gz 75 31 AGATCGGAAGAGCACA XXXXXXXXXXXXX homo_sapiens ../input_files/homo_sapiens/annotation.gtf ../input_files/homo_sapiens/annotation.gtf ../input_files/homo_sapiens/genome.fa ../input_files/homo_sapiens/transcriptome.fa 100 250 10 EndToEnd None A AAAAAAAAAAAAAAAAA XXXXXXXXXXXXXXXXX --fr fr-firststrand str1 str2 XXXXXXXXXXXXX XXXXXXXXXXXXX XXXXXXXXXXXXX XXXXXXXXXXXXX XXXXXXXXXXXXX
sample seqmode fq1 index_size kmer fq1_3p fq1_5p organism gtf genome sd mean multimappers soft_clip pass_mode libtype fq1_polya_3p fq1_polya_5p kallisto_directionality alfa_directionality alfa_plus alfa_minus fq2 fq2_3p fq2_5p fq2_polya_3p fq2_polya_5p
synthetic_10_reads_paired_synthetic_10_reads_paired pe ../input_files/project1/synthetic.mate_1.fastq.gz 75 31 AGATCGGAAGAGCACA XXXXXXXXXXXXX homo_sapiens ../input_files/homo_sapiens/annotation.gtf ../input_files/homo_sapiens/genome.fa 100 250 10 EndToEnd None A AAAAAAAAAAAAAAAAA XXXXXXXXXXXXXXXXX --fr fr-firststrand str1 str2 ../input_files/project1/synthetic.mate_2.fastq.gz AGATCGGAAGAGCGT XXXXXXXXXXXXX XXXXXXXXXXXXXXXXX TTTTTTTTTTTTTTTTT
synthetic_10_reads_mate_1_synthetic_10_reads_mate_1 se ../input_files/project2/synthetic.mate_1.fastq.gz 75 31 AGATCGGAAGAGCACA XXXXXXXXXXXXX homo_sapiens ../input_files/homo_sapiens/annotation.gtf ../input_files/homo_sapiens/genome.fa 100 250 10 EndToEnd None A AAAAAAAAAAAAAAAAA XXXXXXXXXXXXXXXXX --fr fr-firststrand str1 str2 XXXXXXXXXXXXX XXXXXXXXXXXXX XXXXXXXXXXXXX XXXXXXXXXXXXX XXXXXXXXXXXXX
sample seqmode fq1 index_size kmer fq2 fq1_3p fq1_5p fq2_3p fq2_5p organism gtf gtf_filtered genome tr_fasta_filtered sd mean multimappers soft_clip pass_mode libtype kallisto_directionality fq1_polya fq2_polya alfa_directionality alfa_plus alfa_minus
paired_end_R1_on_plus_sense pe XXXXXXXXXXXXX 75 31 XXXXXXXXXXXXX GATCGGAAGAGCACA XXXXXXXXXXXXX AGATCGGAAGAGCGT XXXXXXXXXXXXX homo_sapiens ../input_files/homo_sapiens/quick_start.gtf ../input_files/homo_sapiens/quick_start.gtf XXXXXXXXXXXXX XXXXXXXXXXXXX 100 250 10 EndToEnd None A --fr AAAAAAAAAAAAAAAAA TTTTTTTTTTTTTTTTT fr-firststrand str1 str2
paired_end_R1_on_plus_antisense pe XXXXXXXXXXXXX 75 31 XXXXXXXXXXXXX AGATCGGAAGAGCACA XXXXXXXXXXXXX AGATCGGAAGAGCGT XXXXXXXXXXXXX homo_sapiens ../input_files/homo_sapiens/quick_start.gtf ../input_files/homo_sapiens/quick_start.gtf XXXXXXXXXXXXX XXXXXXXXXXXXX 100 250 10 EndToEnd None A --rf AAAAAAAAAAAAAAAAA TTTTTTTTTTTTTTTTT fr-secondstrand str2 str1
paired_end_R1_on_minus_sense pe XXXXXXXXXXXXX 75 31 XXXXXXXXXXXXX AGATCGGAAGAGCACA XXXXXXXXXXXXX AGATCGGAAGAGCGT XXXXXXXXXXXXX homo_sapiens ../input_files/homo_sapiens/quick_start.gtf ../input_files/homo_sapiens/quick_start.gtf XXXXXXXXXXXXX XXXXXXXXXXXXX 100 250 10 EndToEnd None A --fr AAAAAAAAAAAAAAAAA TTTTTTTTTTTTTTTTT fr-firststrand str1 str2
paired_end_R1_on_minus_antisense pe XXXXXXXXXXXXX 75 31 XXXXXXXXXXXXX AGATCGGAAGAGCACA XXXXXXXXXXXXX AGATCGGAAGAGCGT XXXXXXXXXXXXX homo_sapiens ../input_files/homo_sapiens/quick_start.gtf ../input_files/homo_sapiens/quick_start.gtf XXXXXXXXXXXXX XXXXXXXXXXXXX 100 250 10 EndToEnd None A --rf AAAAAAAAAAAAAAAAA TTTTTTTTTTTTTTTTT fr-secondstrand str2 str1
sample seqmode fq1 index_size kmer fq2 fq1_3p fq1_5p fq2_3p fq2_5p organism gtf genome sd mean multimappers soft_clip pass_mode libtype kallisto_directionality fq1_polya fq2_polya alfa_directionality alfa_plus alfa_minus
paired_end_R1_on_plus_sense pe XXXXXXXXXXXXX 75 31 XXXXXXXXXXXXX GATCGGAAGAGCACA XXXXXXXXXXXXX AGATCGGAAGAGCGT XXXXXXXXXXXXX homo_sapiens ../input_files/homo_sapiens/quick_start.gtf XXXXXXXXXXXXX 100 250 10 EndToEnd None A --fr AAAAAAAAAAAAAAAAA TTTTTTTTTTTTTTTTT fr-firststrand str1 str2
paired_end_R1_on_plus_antisense pe XXXXXXXXXXXXX 75 31 XXXXXXXXXXXXX AGATCGGAAGAGCACA XXXXXXXXXXXXX AGATCGGAAGAGCGT XXXXXXXXXXXXX homo_sapiens ../input_files/homo_sapiens/quick_start.gtf XXXXXXXXXXXXX 100 250 10 EndToEnd None A --rf AAAAAAAAAAAAAAAAA TTTTTTTTTTTTTTTTT fr-secondstrand str2 str1
paired_end_R1_on_minus_sense pe XXXXXXXXXXXXX 75 31 XXXXXXXXXXXXX AGATCGGAAGAGCACA XXXXXXXXXXXXX AGATCGGAAGAGCGT XXXXXXXXXXXXX homo_sapiens ../input_files/homo_sapiens/quick_start.gtf XXXXXXXXXXXXX 100 250 10 EndToEnd None A --fr AAAAAAAAAAAAAAAAA TTTTTTTTTTTTTTTTT fr-firststrand str1 str2
paired_end_R1_on_minus_antisense pe XXXXXXXXXXXXX 75 31 XXXXXXXXXXXXX AGATCGGAAGAGCACA XXXXXXXXXXXXX AGATCGGAAGAGCGT XXXXXXXXXXXXX homo_sapiens ../input_files/homo_sapiens/quick_start.gtf XXXXXXXXXXXXX 100 250 10 EndToEnd None A --rf AAAAAAAAAAAAAAAAA TTTTTTTTTTTTTTTTT fr-secondstrand str2 str1
......@@ -38,15 +38,15 @@ find results/ -type f -name \*\.zip -exec sh -c 'unzip -o {} -d $(dirname {})' \
md5sum --check "expected_output.md5"
# Checksum file generated with
find results/ \
-type f \
-name \*\.gz \
-exec gunzip '{}' \;
find results/ \
-type f \
-name \*\.zip \
-exec sh -c 'unzip -o {} -d $(dirname {})' \;
md5sum $(cat expected_output.files) > expected_output.md5
#find results/ \
# -type f \
# -name \*\.gz \
# -exec gunzip '{}' \;
#find results/ \
# -type f \
# -name \*\.zip \
# -exec sh -c 'unzip -o {} -d $(dirname {})' \;
#md5sum $(cat expected_output.files) > expected_output.md5
# Check whether STAR produces expected alignments
# STAR alignments need to be fully within ground truth alignments for tests to pass; not checking
......
......@@ -9,7 +9,7 @@ cleanup () {
rm -rf ${HOME}/.netrc
rm -rf .snakemake/
rm -rf config.yaml
rm -rf input_table.tsv
rm -rf samples.tsv.labkey
rm -rf samples.tsv
cd $user_dir
echo "Exit status: $rc"
......@@ -31,15 +31,16 @@ EOF
# Run tests
python "../../scripts/labkey_to_snakemake.py" \
--input-dict="../../scripts/labkey_to_snakemake.dict.tsv" \
--labkey-domain="${LABKEY_HOST}" \
--labkey-path="/Zavolan Group/TEST_LABKEY" \
--input-to-output-mapping="../../scripts/labkey_to_snakemake.dict.tsv" \
--resources-dir="../input_files" \
--output-table="samples.tsv" \
--config-file="config.yaml" \
--samples-table="samples.tsv" \
--multimappers='10' \
--remote \
--project-name "TEST_LABKEY" \
--table-name "RNA_Seq_data_template" \
--logo="../../images/logo.128px.png" \
"../input_files"
--debug \
"RNA_Seq_data_template"
# Check if dry run completes
snakemake \
......@@ -48,6 +49,7 @@ snakemake \
--dryrun \
--verbose
md5sum --check "expected_output.md5"
#md5sum --check "expected_output.md5"
# MD5 sums obtained with command:
# md5sum config.yaml samples.tsv > expected_output.md5
md5sum config.yaml samples.tsv
aa583b9bad45eeb520d9d624cca0af78 samples.tsv
c4cda83b069eb7ccb16547e1a9cdb34a config.yaml
\ No newline at end of file
057cbd5757ca7f0b94909eeeca531af3 config.yaml
34422785b7cc77d1aac73d25e767dc2d samples.tsv
......@@ -22,13 +22,13 @@ cd $script_dir/
# Run tests
python "../../scripts/labkey_to_snakemake.py" \
--input-table="input_table.tsv" \
--input-dict="../../scripts/labkey_to_snakemake.dict.tsv" \
--input-to-output-mapping="../../scripts/labkey_to_snakemake.dict.tsv" \
--resources-dir="../input_files" \
--output-table="samples.tsv" \
--config-file="config.yaml" \
--samples-table="samples.tsv" \
--logo="../../images/logo.128px.png" \
--multimappers='10' \
"../input_files"
--logo="../../images/logo.128px.png" \
"input_table.tsv"
# Check if dry run completes
......
......@@ -259,7 +259,7 @@ rule pe_quantification_salmon:
"{sample}",
"{sample}.pe.remove_polya_mate2.fastq.gz"),
gtf = lambda wildcards:
samples_table.loc[wildcards.sample, 'gtf_filtered'],
samples_table.loc[wildcards.sample, 'gtf'],
index = lambda wildcards:
os.path.join(
config["salmon_indexes"],
......
......@@ -214,7 +214,7 @@ rule quantification_salmon:
str(samples_table.loc[wildcards.sample, "kmer"]),
"salmon.idx"),
gtf = lambda wildcards:
samples_table.loc[wildcards.sample, "gtf_filtered"]
samples_table.loc[wildcards.sample, "gtf"]
output:
gn_estimates = os.path.join(
......
......@@ -39,7 +39,6 @@ def main():
parser.add_argument("--url",
help="Url of the lab",
# default='https://zavolan.biozentrum.unibas.ch/',
metavar="STR")
parser.add_argument("--author-name",
......
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