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Commit fc53c215 authored by Alex Kanitz's avatar Alex Kanitz
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Merge branch 'refactor' into 'master' 

Major refactoring before release

Closes #117, #112, #111, #108, #107, #101, and #74

See merge request zavolan_group/pipelines/rhea!62
parents ca049a0c 556f1e12
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1 merge request!62Major refactoring before release
Pipeline #10855 passed
Stage: test
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......@@ -333,4 +333,5 @@ runs/.*
logs/
results/
!tests/test_alfa/results/
tests/input_files/homo_sapiens/genome.fa.fai
.java/
README.md
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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
......
Snakefile
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pipeline_documentation.md
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......@@ -3,39 +3,36 @@ This document describes the individual rules of the pipeline for information pur
## Overview
### General
* read samples table
* create log directories
* **create_index_star**
* **extract_transcriptome**
* **extract_decoys_salmon**
* **concatenate_transcriptome_and_genome**
* **create_index_salmon**
* **create_index_kallisto**
* **extract_transcripts_as_bed12**
* **index_genomic_alignment_samtools**
* **star_rpm**
* **rename_star_rpm_for_alfa**
* **calculate_TIN_scores**
* **merge_TIN_scores**
* **plot_TIN_scores**
* **salmon_quantmerge_genes**
* **salmon_quantmerge_transcripts**
* **generate_alfa_index**
* **alfa_qc**
* **alfa_qc_all_samples**
* **alfa_concat_results**
* **prepare_files_for_report**
* **prepare_MultiQC_config**
* **MULTIQC_report**
* [read samples table](#read-samples-table)
* [create log directories](#create-log-directories)
* **[create_index_star](#create_index_star)**
* **[extract_transcriptome](#extract_transcriptome)**
* **[create_index_salmon](#create_index_salmon)**
* **[create_index_kallisto](#create_index_kallisto)**
* **[extract_transcripts_as_bed12](#extract_transcripts_as_bed12)**
* **[index_genomic_alignment_samtools](#index_genomic_alignment_samtools)**
* **[star_rpm](#star_rpm)**
* **[rename_star_rpm_for_alfa](#rename_star_rpm_for_alfa)**
* **[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)**
* **[generate_alfa_index](#generate_alfa_index)**
* **[alfa_qc](#alfa_qc)**
* **[alfa_qc_all_samples](#alfa_qc_all_samples)**
* **[prepare_files_for_report](#prepare_files_for_report)**
* **[prepare_MultiQC_config](#prepare_MultiQC_config)**
* **[MULTIQC_report](#MULTIQC_report)**
* **[sort_bed_4_big](#sort_bed_4_big)**
### Sequencing mode specific
* **(pe_)fastqc**
* **(pe_)remove_adapters_cutadapt**
* **(pe_)remove_polya_cutadapt**
* **(pe_)map_genome_star**
* **(pe_)quantification_salmon**
* **(pe_)genome_quantification_kallisto**
* **[(pe_)fastqc](#(pe_)fastqc)**
* **[(pe_)remove_adapters_cutadapt](#(pe_)remove_adapters_cutadapt)**
* **[(pe_)remove_polya_cutadapt](#(pe_)remove_polya_cutadapt)**
* **[(pe_)map_genome_star](#(pe_)map_genome_star)**
* **[(pe_)quantification_salmon](#(pe_)quantification_salmon)**
* **[(pe_)genome_quantification_kallisto](#(pe_)genome_quantification_kallisto)**
......@@ -100,23 +97,7 @@ Create transcriptome from genome and gene annotations using [gffread](https://gi
**Input:** `genome` and `gtf` of the input samples table
**Output:** transcriptome fasta file.
#### extract_decoys_salmon
Salmon indexing requires the names of the genome targets (https://combine-lab.github.io/alevin-tutorial/2019/selective-alignment/). Extract target names from the genome.
**Input:** `genome` of the input samples table
**Output:** text file with the genome targert names
#### concatenate_transcriptome_and_genome
Salmon indexing requires concatenated transcriptome and genome reference file (https://combine-lab.github.io/alevin-tutorial/2019/selective-alignment/).
**Input:** `genome` of the input samples table and extracted transcriptome
**Output:** fasta file with concatenated genome and transcriptome
#### create_index_salmon
Create index for [Salmon](https://salmon.readthedocs.io/en/latest/salmon.html) quantification. Salmon index of transcriptome, required for mapping-based mode of Salmon. The index is created via an auxiliary k-mer hash over k-mers of length 31. While mapping algorithms will make use of arbitrarily long matches between the query and reference, the k-mer size selected here will act as the minimum acceptable length for a valid match. A k-mer size of 31 seems to work well for reads of 75bp or longer, although smaller size might improve sensitivity. A smaller k-mer size is suggested when working with shorter reads.
......@@ -263,6 +244,18 @@ Interactive report of the various workflow steps. [MultiQC](https://multiqc.info
**Input:** Config file fort MultiQC in .yaml format
**Output:** Directory with automatically generated HTML report
#### sort_bed_4_big
Sorts bedgraph files for creating bigWig files. Using [bedtools sortBed](https://bedtools.readthedocs.io/en/latest/content/tools/sort.html)
**Input:** bedgraph files from `rename_star_rpm_for_alfa`
**Output:** sorted bedgraph files
#### prepare_bigWig
Check out some infos on bigWig files and [bedGraphtobigWig](http://genome.ucsc.edu/goldenPath/help/bigWig.html).
**Input:** sorted bedgraph files, chromosome sizes from create_STAR_index
**Output:** one bigWig file per sample and strand
### Sequencing mode specific rules
......
scripts/labkey_to_snakemake.py
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tests/input_files/config.yaml
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---
samples: "../input_files/samples.tsv"
output_dir: "results/"
log_dir: "logs/"
kallisto_indexes: "results/kallisto_indexes/"
salmon_indexes: "results/salmon_indexes/"
star_indexes: "results/star_indexes/"
alfa_indexes: "results/alfa_indexes/"
...
output_dir: "results"
log_dir: "logs"
kallisto_indexes: "results/kallisto_indexes"
salmon_indexes: "results/salmon_indexes"
star_indexes: "results/star_indexes"
alfa_indexes: "results/alfa_indexes"
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
tests/input_files/config_alfa.yaml
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......@@ -6,4 +6,7 @@
salmon_indexes: "results/salmon_indexes/"
star_indexes: "results/star_indexes/"
alfa_indexes: "results/alfa_indexes/"
report_description: "No description provided by user"
report_logo: "../../images/logo.128px.png"
report_url: "https://zavolan.biozentrum.unibas.ch/"
...
tests/input_files/samples.tsv
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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 fq2 fq2_3p fq2_5p fq2_polya_3p fq2_polya_5p
synthetic_10_reads_paired_synthetic_10_reads_paired paired_end ../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 ../input_files/project1/synthetic.mate_2.fastq.gz AGATCGGAAGAGCGT XXXXXXXXXXXXX XXXXXXXXXXXXXXXXX TTTTTTTTTTTTTTTTT
synthetic_10_reads_mate_1_synthetic_10_reads_mate_1 single_end ../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 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
tests/input_files/samples_alfa.tsv
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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
paired_end_R1_on_plus_sense paired_end 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
paired_end_R1_on_plus_antisense paired_end 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
paired_end_R1_on_minus_sense paired_end 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
paired_end_R1_on_minus_antisense paired_end 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
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
tests/test_alfa/expected_output.md5
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90e42aa46890e9cd0a47800428699fbf results/alfa_indexes/homo_sapiens/75/ALFA/sorted_genes.stranded.ALFA_index
ccc3cf5a57fddb0d469e597d4376b1bf results/alfa_indexes/homo_sapiens/75/ALFA/sorted_genes.unstranded.ALFA_index
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c406c1800d3690dd774aaa7e3c190523 results/paired_end/paired_end_R1_on_minus_sense/ALFA/Unique/paired_end_R1_on_minus_sense.ALFA_feature_counts.tsv
c406c1800d3690dd774aaa7e3c190523 results/paired_end/paired_end_R1_on_plus_antisense/ALFA/Unique/paired_end_R1_on_plus_antisense.ALFA_feature_counts.tsv
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