diff --git a/Snakefile b/Snakefile
index c8619f4bbd2c6ddb42624bd38a9fe74172d1afef..2ee4d730ca85cd6f0de07b50e6946d209d6521d8 100644
--- a/Snakefile
+++ b/Snakefile
@@ -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 \
diff --git a/pipeline_documentation.md b/pipeline_documentation.md
index 17decd1845b6a8c54bec126d401db7ac20ed2689..c5e45a9158aa09403a97d5a825c969bab97c3c9e 100644
--- a/pipeline_documentation.md
+++ b/pipeline_documentation.md
@@ -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).