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Commit 7cdef5af authored by BIOPZ-Bak Maciej's avatar BIOPZ-Bak Maciej
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ci: test new multiqc container

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1 merge request!79MultiQC plugins for TIN scores and ALFA
Pipeline #11939 failed
Stage: test
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View file @ 7cdef5af
......@@ -546,101 +546,6 @@ rule calculate_TIN_scores:
-n 100 > {output.TIN_score};) 2> {log.stderr}"
rule merge_TIN_scores:
"""
Merge TIN scores tables
"""
input:
TIN_score = expand(
os.path.join(
config['output_dir'],
"samples",
"{sample}",
"TIN",
"TIN_score.tsv"),
sample=pd.unique(samples_table.index.values)),
output:
TIN_scores_merged = os.path.join(
config['output_dir'],
"TIN_scores_merged.tsv")
log:
stderr = os.path.join(
config['log_dir'],
"merge_TIN_scores.stderr.log"),
stdout = os.path.join(
config["log_dir"],
"merge_TIN_scores.stdout.log")
params:
TIN_score_merged_paths = ",".join(expand(
os.path.join(
config['output_dir'],
"samples",
"{sample}",
"TIN",
"TIN_score.tsv"),
zip,
sample=[i for i in pd.unique(samples_table.index.values)],
seqmode=[get_sample('seqmode',
search_id='index',
search_value=i) for i in pd.unique(samples_table.index.values)]))
threads: 1
singularity:
"docker://zavolab/tin_score_calculation:0.2.0-slim"
shell:
"(tin_score_merge.py \
--input-files {params.TIN_score_merged_paths} \
--output-file {output.TIN_scores_merged}) \
1> {log.stdout} 2> {log.stderr}"
rule plot_TIN_scores:
"""
Generate TIN scores boxplots
"""
input:
TIN_scores_merged = os.path.join(
config['output_dir'],
"TIN_scores_merged.tsv"),
output:
TIN_boxplot_PNG = os.path.join(
config['output_dir'],
"TIN_scores_boxplot_mqc.png"),
TIN_boxplot_PDF = os.path.join(
config['output_dir'],
"TIN_scores_boxplot_mqc.pdf")
params:
TIN_boxplot_prefix = os.path.join(
config['output_dir'],
"TIN_scores_boxplot_mqc")
log:
stderr = os.path.join(
config['log_dir'],
"plot_TIN_scores.stderr.log"),
stdout = os.path.join(
config["log_dir"],
"plot_TIN_scores.stdout.log")
threads: 1
singularity:
"docker://zavolab/tin_score_calculation:0.2.0-slim"
shell:
"(tin_score_plot.py \
--input-file {input.TIN_scores_merged} \
--output-file-prefix {params.TIN_boxplot_prefix}) \
1> {log.stdout} 2> {log.stderr}"
rule salmon_quantmerge_genes:
'''
Merge gene quantifications into a single file
......@@ -1318,83 +1223,6 @@ rule alfa_qc:
-s {params.alfa_orientation}) &> {log}"
rule alfa_qc_all_samples:
'''
Run ALFA from stranded bedgraph files on all samples
'''
input:
tables = lambda wildcards:
expand(
os.path.join(
config["output_dir"],
"samples",
"{sample}",
"ALFA",
"{unique}",
"{sample}.ALFA_feature_counts.tsv"),
sample=pd.unique(samples_table.index.values),
unique=wildcards.unique)
output:
biotypes = os.path.join(
config["output_dir"],
"ALFA",
"{unique}",
"ALFA_plots.Biotypes.pdf"),
categories = os.path.join(
config["output_dir"],
"ALFA",
"{unique}",
"ALFA_plots.Categories.pdf")
params:
out_dir = lambda wildcards, output:
os.path.dirname(output.biotypes)
log:
os.path.join(
config["log_dir"],
"alfa_qc_all_samples.{unique}.log")
singularity:
"docker://zavolab/alfa:1.1.1-slim"
shell:
"(alfa -c {input.tables} -o {params.out_dir}) &> {log}"
rule alfa_concat_results:
input:
expand(
os.path.join(
config["output_dir"],
"ALFA",
"{unique}",
"ALFA_plots.{annotation}.pdf"),
unique=["Unique", "UniqueMultiple"],
annotation=["Categories", "Biotypes"])
output:
os.path.join(
config["output_dir"],
"ALFA",
"ALFA_plots_mqc.png")
params:
density = 300
log:
os.path.join(
config["log_dir"],
"alfa_qc_all_samples.concat.log")
singularity:
"docker://zavolab/imagemagick:7.0.8"
shell:
"(convert -append -density {params.density} \
{input} {output}) &> {log}"
rule prepare_multiqc_config:
'''
Prepare config for the MultiQC
......@@ -1471,18 +1299,26 @@ rule multiqc_report:
seqmode=[get_sample('seqmode', search_id='index', search_value=i)
for i in pd.unique(samples_table.index.values)]),
TIN_boxplot_PNG = os.path.join(
config['output_dir'],
"TIN_scores_boxplot_mqc.png"),
TIN_boxplot_PDF = os.path.join(
config['output_dir'],
"TIN_scores_boxplot_mqc.pdf"),
TIN_score = expand(
os.path.join(
config['output_dir'],
"samples",
"{sample}",
"TIN",
"TIN_score.tsv"),
sample=pd.unique(samples_table.index.values)),
alfa_concat_out = os.path.join(
config["output_dir"],
"ALFA",
"ALFA_plots_mqc.png"),
tables = lambda wildcards:
expand(
os.path.join(
config["output_dir"],
"samples",
"{sample}",
"ALFA",
"{unique}",
"{sample}.ALFA_feature_counts.tsv"),
sample=pd.unique(samples_table.index.values),
unique=["Unique", "UniqueMultiple"]),
zpca_salmon = expand(os.path.join(
config["output_dir"],
......@@ -1521,7 +1357,7 @@ rule multiqc_report:
"multiqc_report.stdout.log")
singularity:
"docker://ewels/multiqc:1.7"
"docker://zavolab/multiqc:1.9"
shell:
"(multiqc \
......
pipeline_documentation.md
+ 0
− 48
View file @ 7cdef5af
......@@ -26,8 +26,6 @@ on installation and usage please see [here](README.md).
- [**sort_bed_4_big**](#sort_bed_4_big)
- [**prepare_bigWig**](#prepare_bigwig)
- [**calculate_TIN_scores**](#calculate_tin_scores)
- [**merge_TIN_scores**](#merge_tin_scores)
- [**plot_TIN_scores**](#plot_tin_scores)
- [**salmon_quantmerge_genes**](#salmon_quantmerge_genes)
- [**salmon_quantmerge_transcripts**](#salmon_quantmerge_transcripts)
- [**kallisto_merge_genes**](#kallisto_merge_genes)
......@@ -36,8 +34,6 @@ on installation and usage please see [here](README.md).
- [**pca_salmon**](#pca_salmon)
- [**generate_alfa_index**](#generate_alfa_index)
- [**alfa_qc**](#alfa_qc)
- [**alfa_qc_all_samples**](#alfa_qc_all_samples)
- [**alfa_concat_results**](#alfa_concat_results)
- [**prepare_multiqc_config**](#prepare_multiqc_config)
- [**multiqc_report**](#multiqc_report)
- [**finish**](#finish)
......@@ -365,29 +361,6 @@ Calculates the Transcript Integrity Number (TIN) for each transcript with
- TIN score table (custom `tsv`); used in
[**merge_TIN_scores**](#merge_tin_scores)
#### `merge_TIN_scores`
Merges TIN score tables for all samples with [custom script][custom-script-tin].
- **Input**
- TIN score table (custom `tsv`); per sample; from
[**calculate_TIN_scores**](#calculate_tin_scores)
- **Output**
- TIN score table (custom `tsv`); for all samples; used in
[**plot_TIN_scores**](#plot_tin_scores)
#### `plot_TIN_scores`
Generate sample-wise [box plots](https://en.wikipedia.org/wiki/Box_plot) of
TIN scores with [custom script][custom-script-tin].
- **Input**
- TIN score table (custom `tsv`); for all samples; from
[**merge_TIN_scores**](#merge_tin_scores)
- **Output**
- TIN score box plots (`.pdf` and `.png`); used in
[**multiqc_report**](#multiqc_report)
#### `salmon_quantmerge_genes`
Merge gene-level expression estimates for all samples with
......@@ -502,27 +475,6 @@ Annotate alignments with [**ALFA**](#third-party-software-used).
- Feature counts table (custom `.tsv`); used in
[**alfa_qc_all_samples**](#alfa_qc_all_samples)
#### `alfa_qc_all_samples`
Combines output of all samples with [**ALFA**](#third-party-software-used).
- **Input**
- Feature counts table (custom `.tsv`); from [**alfa_qc**](#alfa_qc)
- **Output**
- Figures for biotypes and feature categories (`.pdf`); summarized for all
samples together; used in [**alfa_concat_results**](#alfa_concat_results)
#### `alfa_concat_results`
Concatenate and convert ALFA output plots into single plot with
[**ImageMagick**](#third-party-software-used).
- **Input**
- Figures for biotypes and feature categories (`.pdf`); for individual and
summarized for all samples
- **Output**
- ALFA plot (`.png`), combined; used in [**multiqc_report**](#multiqc_report)
#### `prepare_multiqc_config`
Prepare config file for [**MultiQC**](#third-party-software-used).
......
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