From 10885dca3d321520a47af242f362dfed4aebff1a Mon Sep 17 00:00:00 2001
From: BIOPZ-Gypas Foivos <foivos.gypas@unibas.ch>
Date: Fri, 11 Jun 2021 15:00:37 +0000
Subject: [PATCH] Add conda support in ZARP
---
.gitlab-ci.yml | 3 +-
README.md | 29 +++--
tests/test_create_dag_image/test.sh | 2 +-
tests/test_create_rule_graph/test.sh | 2 +-
tests/test_integration_workflow/test.local.sh | 4 +-
.../test.local.sh | 4 +-
.../expected_output.files | 114 ++++++++++++++++++
.../expected_output.md5 | 96 +++++++++++++++
.../test.local.sh | 91 ++++++++++++++
.../test.slurm.sh | 94 +++++++++++++++
.../test_scripts_prepare_inputs_table/test.sh | 2 +-
Snakefile => workflow/Snakefile | 65 +++++++++-
workflow/envs/STAR.yaml | 7 ++
workflow/envs/alfa.yaml | 7 ++
workflow/envs/bedtools.yaml | 7 ++
workflow/envs/cutadapt.yaml | 7 ++
workflow/envs/fastqc.yaml | 7 ++
workflow/envs/gffread.yaml | 7 ++
workflow/envs/kallisto.yaml | 7 ++
workflow/envs/r-merge-kallisto.yaml | 7 ++
workflow/envs/salmon.yaml | 7 ++
workflow/envs/samtools.yaml | 7 ++
workflow/envs/tin-score-calculation.yaml | 7 ++
workflow/envs/ucsc-bedgraphtobigwig.yaml | 7 ++
workflow/envs/zavolan-multiqc-plugins.yaml | 7 ++
workflow/envs/zgtf.yaml | 7 ++
workflow/envs/zpca.yaml | 7 ++
workflow/rules/paired_end.snakefile.smk | 15 +++
workflow/rules/single_end.snakefile.smk | 15 +++
29 files changed, 620 insertions(+), 21 deletions(-)
create mode 100644 tests/test_integration_workflow_with_conda/expected_output.files
create mode 100644 tests/test_integration_workflow_with_conda/expected_output.md5
create mode 100755 tests/test_integration_workflow_with_conda/test.local.sh
create mode 100755 tests/test_integration_workflow_with_conda/test.slurm.sh
rename Snakefile => workflow/Snakefile (96%)
create mode 100644 workflow/envs/STAR.yaml
create mode 100644 workflow/envs/alfa.yaml
create mode 100644 workflow/envs/bedtools.yaml
create mode 100644 workflow/envs/cutadapt.yaml
create mode 100644 workflow/envs/fastqc.yaml
create mode 100644 workflow/envs/gffread.yaml
create mode 100644 workflow/envs/kallisto.yaml
create mode 100644 workflow/envs/r-merge-kallisto.yaml
create mode 100644 workflow/envs/salmon.yaml
create mode 100644 workflow/envs/samtools.yaml
create mode 100644 workflow/envs/tin-score-calculation.yaml
create mode 100644 workflow/envs/ucsc-bedgraphtobigwig.yaml
create mode 100644 workflow/envs/zavolan-multiqc-plugins.yaml
create mode 100644 workflow/envs/zgtf.yaml
create mode 100644 workflow/envs/zpca.yaml
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 00dd3ed..bd07e11 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -13,9 +13,10 @@ test:
# add unit tests here
# add script tests here
- bash tests/test_scripts_prepare_inputs_table/test.sh
- #- bash tests/test_scripts_prepare_inputs_labkey/test.sh
+ # - bash tests/test_scripts_prepare_inputs_labkey/test.sh
#- bash tests/test_alfa/test.sh
# add integration tests here
+ - bash tests/test_integration_workflow_with_conda/test.local.sh
- bash tests/test_create_dag_image/test.sh
- bash tests/test_create_rule_graph/test.sh
- bash tests/test_integration_workflow/test.local.sh
diff --git a/README.md b/README.md
index 628833d..68a667e 100644
--- a/README.md
+++ b/README.md
@@ -14,7 +14,7 @@ Below is a schematic representation of the individual steps of the workflow
> ![rule_graph][rule-graph]
For a more detailed description of each step, please refer to the [workflow
-documentation][workflow-documentation].
+documentation][pipeline-documentation].
## Requirements
@@ -48,12 +48,8 @@ Other versions are not guaranteed to work as expected.
### Installing dependencies
For improved reproducibility and reusability of the workflow,
-each individual step of the workflow runs in its own [Singularity][singularity]
-container. As a consequence, running this workflow has very few
-individual dependencies. However, it requires Singularity to be installed
-on the system where the workflow is executed. As the functional installation of
-Singularity requires root privileges, and Conda currently only provides
-Singularity for Linux architectures, the installation instructions are
+each individual step of the workflow runs either in its own [Singularity][singularity]
+container or in its own [Conda][conda] virtual environemnt. As a consequence, running this workflow has very few individual dependencies. However, for the **container execution** it requires Singularity to be installed on the system where the workflow is executed. As the functional installation of Singularity requires root privileges, and Conda currently only provides Singularity for Linux architectures, the installation instructions are
slightly different depending on your system/setup:
#### For most users
@@ -115,12 +111,17 @@ need to be installed.
### Test workflow on local machine
-Execute the following command to run the test workflow on your local machine:
+Execute the following command to run the test workflow on your local machine (with singularity):
```bash
bash tests/test_integration_workflow/test.local.sh
```
+Alternatively execute the following command to run the test workflow on your local machine (with conda):
+```bash
+bash tests/test_integration_workflow_with_conda/test.local.sh
+```
+
### Test workflow via Slurm
Execute the following command to run the test workflow on a
@@ -130,6 +131,12 @@ Execute the following command to run the test workflow on a
bash tests/test_integration_workflow/test.slurm.sh
```
+or
+
+```bash
+bash tests/test_integration_workflow_with_conda/test.slurm.sh
+```
+
> **NOTE:** Depending on the configuration of your Slurm installation or if
> using a different workload manager, you may need to adapt file `cluster.json`
> and the arguments to options `--config` and `--cores` in the file
@@ -177,7 +184,7 @@ your run.
cat << "EOF" > run.sh
#!/bin/bash
snakemake \
- --snakefile="../../snakemake/Snakefile" \
+ --snakefile="/path/to/Snakefile" \
--configfile="config.yaml" \
--cores=4 \
--printshellcmds \
@@ -198,7 +205,7 @@ your run.
#!/bin/bash
mkdir -p logs/cluster_log
snakemake \
- --snakefile="../../snakemake/Snakefile" \
+ --snakefile="/path/to/Snakefile" \
--configfile="config.yaml" \
--cluster-config="cluster.json" \
--cluster="sbatch --cpus-per-task={cluster.threads} --mem={cluster.mem} --qos={cluster.queue} --time={cluster.time} --job-name={cluster.name} -o {cluster.out} -p scicore" \
@@ -210,6 +217,8 @@ your run.
EOF
```
+ When running the pipeline with conda you should use the `--use-conda` flag instead of `--use-singularity` and `--singularity-args`.
+
5. Start your workflow run:
```bash
diff --git a/tests/test_create_dag_image/test.sh b/tests/test_create_dag_image/test.sh
index 1c954dd..87b5dad 100755
--- a/tests/test_create_dag_image/test.sh
+++ b/tests/test_create_dag_image/test.sh
@@ -20,7 +20,7 @@ cd $script_dir
# Run tests
snakemake \
- --snakefile="../../Snakefile" \
+ --snakefile="../../workflow/Snakefile" \
--configfile="../input_files/config.yaml" \
--dag \
--printshellcmds \
diff --git a/tests/test_create_rule_graph/test.sh b/tests/test_create_rule_graph/test.sh
index 287e08d..4e53450 100755
--- a/tests/test_create_rule_graph/test.sh
+++ b/tests/test_create_rule_graph/test.sh
@@ -20,7 +20,7 @@ cd $script_dir
# Run tests
snakemake \
- --snakefile="../../Snakefile" \
+ --snakefile="../../workflow/Snakefile" \
--configfile="../input_files/config.yaml" \
--rulegraph \
--printshellcmds \
diff --git a/tests/test_integration_workflow/test.local.sh b/tests/test_integration_workflow/test.local.sh
index 69b179d..201c4ca 100755
--- a/tests/test_integration_workflow/test.local.sh
+++ b/tests/test_integration_workflow/test.local.sh
@@ -26,7 +26,7 @@ cd $script_dir
# Run tests
snakemake \
- --snakefile="../../Snakefile" \
+ --snakefile="../../workflow/Snakefile" \
--configfile="../input_files/config.yaml" \
--cores=4 \
--printshellcmds \
@@ -39,7 +39,7 @@ snakemake \
# Create a Snakemake report after the workflow execution
snakemake \
- --snakefile="../../Snakefile" \
+ --snakefile="../../workflow/Snakefile" \
--configfile="../input_files/config.yaml" \
--report="snakemake_report.html"
diff --git a/tests/test_integration_workflow_multiple_lanes/test.local.sh b/tests/test_integration_workflow_multiple_lanes/test.local.sh
index fd45fa4..48b95e8 100755
--- a/tests/test_integration_workflow_multiple_lanes/test.local.sh
+++ b/tests/test_integration_workflow_multiple_lanes/test.local.sh
@@ -26,7 +26,7 @@ cd $script_dir
# Run tests
snakemake \
- --snakefile="../../Snakefile" \
+ --snakefile="../../workflow/Snakefile" \
--configfile="../input_files/config.mutliple_lanes.yml" \
--cores=4 \
--printshellcmds \
@@ -39,7 +39,7 @@ snakemake \
# Create a Snakemake report after the workflow execution
snakemake \
- --snakefile="../../Snakefile" \
+ --snakefile="../../workflow/Snakefile" \
--configfile="../input_files/config.mutliple_lanes.yml" \
--report="snakemake_report.html"
diff --git a/tests/test_integration_workflow_with_conda/expected_output.files b/tests/test_integration_workflow_with_conda/expected_output.files
new file mode 100644
index 0000000..a9026e6
--- /dev/null
+++ b/tests/test_integration_workflow_with_conda/expected_output.files
@@ -0,0 +1,114 @@
+results/kallisto_indexes/homo_sapiens/kallisto.idx
+results/salmon_indexes/homo_sapiens/31/salmon.idx/versionInfo.json
+results/salmon_indexes/homo_sapiens/31/salmon.idx/duplicate_clusters.tsv
+results/salmon_indexes/homo_sapiens/31/salmon.idx/info.json
+results/star_indexes/homo_sapiens/75/STAR_index/chrLength.txt
+results/star_indexes/homo_sapiens/75/STAR_index/chrNameLength.txt
+results/star_indexes/homo_sapiens/75/STAR_index/chrName.txt
+results/star_indexes/homo_sapiens/75/STAR_index/chrStart.txt
+results/star_indexes/homo_sapiens/75/STAR_index/exonGeTrInfo.tab
+results/star_indexes/homo_sapiens/75/STAR_index/exonInfo.tab
+results/star_indexes/homo_sapiens/75/STAR_index/geneInfo.tab
+results/star_indexes/homo_sapiens/75/STAR_index/Genome
+results/star_indexes/homo_sapiens/75/STAR_index/SA
+results/star_indexes/homo_sapiens/75/STAR_index/SAindex
+results/star_indexes/homo_sapiens/75/STAR_index/sjdbInfo.txt
+results/star_indexes/homo_sapiens/75/STAR_index/sjdbList.fromGTF.out.tab
+results/star_indexes/homo_sapiens/75/STAR_index/sjdbList.out.tab
+results/star_indexes/homo_sapiens/75/STAR_index/transcriptInfo.tab
+results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.pe.remove_adapters_mate1.fastq
+results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.pe.remove_polya_mate1.fastq
+results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.pe.remove_adapters_mate2.fastq
+results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.pe.remove_polya_mate2.fastq
+results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/map_genome/synthetic_10_reads_paired_synthetic_10_reads_paired.pe.SJ.out.tab
+results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq1/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1_fastqc/fastqc_data.txt
+results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq1/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1_fastqc/fastqc.fo
+results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq1/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1_fastqc/summary.txt
+results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq2/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2_fastqc/fastqc_data.txt
+results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq2/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2_fastqc/fastqc.fo
+results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq2/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2_fastqc/summary.txt
+results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq1/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1_fastqc/Images/adapter_content.png
+results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq1/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1_fastqc/Images/duplication_levels.png
+results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq1/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1_fastqc/Images/per_base_n_content.png
+results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq1/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1_fastqc/Images/per_base_quality.png
+results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq1/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1_fastqc/Images/per_base_sequence_content.png
+results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq1/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1_fastqc/Images/per_sequence_gc_content.png
+results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq1/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1_fastqc/Images/per_sequence_quality.png
+results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq1/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1_fastqc/Images/per_tile_quality.png
+results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq1/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1_fastqc/Images/sequence_length_distribution.png
+results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq2/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2_fastqc/Images/adapter_content.png
+results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq2/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2_fastqc/Images/duplication_levels.png
+results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq2/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2_fastqc/Images/per_base_n_content.png
+results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq2/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2_fastqc/Images/per_base_quality.png
+results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq2/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2_fastqc/Images/per_base_sequence_content.png
+results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq2/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2_fastqc/Images/per_sequence_gc_content.png
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+results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/quant_kallisto/abundance.tsv
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+results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.salmon.pe/aux_info/ambig_info.tsv
+results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.salmon.pe/aux_info/expected_bias
+results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.salmon.pe/aux_info/observed_bias
+results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.salmon.pe/aux_info/observed_bias_3p
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+results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.salmon.se/aux_info/ambig_info.tsv
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+results/transcriptome/homo_sapiens/transcriptome.fa
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+results/alfa_indexes/homo_sapiens/75/ALFA/sorted_genes.unstranded.ALFA_index
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\ No newline at end of file
diff --git a/tests/test_integration_workflow_with_conda/expected_output.md5 b/tests/test_integration_workflow_with_conda/expected_output.md5
new file mode 100644
index 0000000..266f992
--- /dev/null
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diff --git a/tests/test_integration_workflow_with_conda/test.local.sh b/tests/test_integration_workflow_with_conda/test.local.sh
new file mode 100755
index 0000000..8a29108
--- /dev/null
+++ b/tests/test_integration_workflow_with_conda/test.local.sh
@@ -0,0 +1,91 @@
+#!/bin/bash
+
+# Tear down test environment
+cleanup () {
+ rc=$?
+ rm -rf .cache/
+ rm -rf .config/
+ rm -rf .fontconfig/
+ rm -rf .java/
+ rm -rf .snakemake/
+ rm -rf logs/
+ rm -rf results/
+ rm -rf snakemake_report.html
+ cd $user_dir
+ echo "Exit status: $rc"
+}
+trap cleanup EXIT
+
+# Set up test environment
+set -eo pipefail # ensures that script exits at first command that exits with non-zero status
+set -u # ensures that script exits when unset variables are used
+set -x # facilitates debugging by printing out executed commands
+user_dir=$PWD
+script_dir="$(cd "$(dirname "${BASH_SOURCE[0]}")" >/dev/null 2>&1 && pwd)"
+cd $script_dir
+
+# Run tests
+snakemake \
+ --snakefile="../../workflow/Snakefile" \
+ --configfile="../input_files/config.yaml" \
+ --cores=4 \
+ --printshellcmds \
+ --rerun-incomplete \
+ --use-conda \
+ --notemp \
+ --no-hooks \
+ --verbose
+
+# Create a Snakemake report after the workflow execution
+snakemake \
+ --snakefile="../../workflow/Snakefile" \
+ --configfile="../input_files/config.yaml" \
+ --report="snakemake_report.html"
+
+# Check md5 sum of some output files
+find results/ -type f -name \*\.gz -exec gunzip '{}' \;
+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 $(cat expected_output.files) > expected_output.md5
+
+# Check whether STAR produces expected alignments
+# STAR alignments need to be fully within ground truth alignments for tests to pass; not checking
+# vice versa because processing might cut off parts of reads (if testing STAR directly, add '-f 1'
+# as additional option)
+echo "Verifying STAR output"
+result=$(bedtools intersect -F 1 -v -bed \
+ -a ../input_files/synthetic.mate_1.bed \
+ -b results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/map_genome/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.se.Aligned.sortedByCoord.out.bam \
+ | wc -l)
+if [ $result != "0" ]; then
+ echo "Alignments for mate 1 reads are not consistent with ground truth"
+ exit 1
+fi
+result=$(bedtools intersect -F 1 -v -bed \
+ -a <(cat ../input_files/synthetic.mate_1.bed ../input_files/synthetic.mate_2.bed) \
+ -b results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/map_genome/synthetic_10_reads_paired_synthetic_10_reads_paired.pe.Aligned.sortedByCoord.out.bam \
+ | wc -l)
+if [ $result != "0" ]; then
+ echo "Alignments for mate 1 reads are not consistent with ground truth"
+ exit 1
+fi
+
+# Check whether Salmon assigns reads to expected genes
+echo "Verifying Salmon output"
+diff \
+ <(cat results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.salmon.se/quant.genes.sf | cut -f1,5 | tail -n +2 | sort -k1,1) \
+ <(cat ../input_files/synthetic.mate_1.bed | cut -f7 | sort | uniq -c | sort -k2nr | awk '{printf($2"\t"$1"\n")}')
+diff \
+ <(cat results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.salmon.pe/quant.genes.sf | cut -f1,5 | tail -n +2 | sort -k1,1) \
+ <(cat ../input_files/synthetic.mate_1.bed | cut -f7 | sort | uniq -c | sort -k2nr | awk '{printf($2"\t"$1"\n")}')
+
diff --git a/tests/test_integration_workflow_with_conda/test.slurm.sh b/tests/test_integration_workflow_with_conda/test.slurm.sh
new file mode 100755
index 0000000..e4a7009
--- /dev/null
+++ b/tests/test_integration_workflow_with_conda/test.slurm.sh
@@ -0,0 +1,94 @@
+#!/bin/bash
+
+# Tear down test environment
+cleanup () {
+ rc=$?
+ # rm -rf .cache/
+ # rm -rf .config/
+ # rm -rf .fontconfig/
+ # rm -rf .java/
+ # rm -rf .snakemake/
+ # rm -rf logs/
+ # rm -rf results/
+ # rm -rf snakemake_report.html
+ cd $user_dir
+ echo "Exit status: $rc"
+}
+trap cleanup EXIT
+
+# Set up test environment
+set -eo pipefail # ensures that script exits at first command that exits with non-zero status
+set -u # ensures that script exits when unset variables are used
+set -x # facilitates debugging by printing out executed commands
+user_dir=$PWD
+script_dir="$(cd "$(dirname "${BASH_SOURCE[0]}")" >/dev/null 2>&1 && pwd)"
+cd $script_dir
+
+# Run tests
+snakemake \
+ --snakefile="../../Snakefile" \
+ --configfile="../input_files/config.yaml" \
+ --cluster-config="../input_files/cluster.json" \
+ --cluster="sbatch --cpus-per-task={cluster.threads} --mem={cluster.mem} --qos={cluster.queue} --time={cluster.time} --job-name={cluster.name} -o {cluster.out} -p scicore" \
+ --cores=256 \
+ --printshellcmds \
+ --rerun-incomplete \
+ --use-conda \
+ --notemp \
+ --no-hooks \
+ --verbose
+
+# Create a Snakemake report after the workflow execution
+snakemake \
+ --snakefile="../../Snakefile" \
+ --configfile="../input_files/config.yaml" \
+ --report="snakemake_report.html"
+
+# Check md5 sum of some output files
+find results/ -type f -name \*\.gz -exec gunzip '{}' \;
+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 $(cat expected_output.files) > expected_output.md5
+
+# Check whether STAR produces expected alignments
+# STAR alignments need to be fully within ground truth alignments for tests to pass; not checking
+# vice versa because processing might cut off parts of reads (if testing STAR directly, add '-f 1'
+# as additional option)
+echo "Verifying STAR output"
+result=$(bedtools intersect -F 1 -v -bed \
+ -a ../input_files/synthetic.mate_1.bed \
+ -b results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/map_genome/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.se.Aligned.sortedByCoord.out.bam \
+ | wc -l)
+if [ $result != "0" ]; then
+ echo "Alignments for mate 1 reads are not consistent with ground truth"
+ exit 1
+fi
+result=$(bedtools intersect -F 1 -v -bed \
+ -a <(cat ../input_files/synthetic.mate_1.bed ../input_files/synthetic.mate_2.bed) \
+ -b results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/map_genome/synthetic_10_reads_paired_synthetic_10_reads_paired.pe.Aligned.sortedByCoord.out.bam \
+ | wc -l)
+if [ $result != "0" ]; then
+ echo "Alignments for mate 1 reads are not consistent with ground truth"
+ exit 1
+fi
+
+# Check whether Salmon assigns reads to expected genes
+echo "Verifying Salmon output"
+diff \
+ <(cat results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.salmon.se/quant.genes.sf | cut -f1,5 | tail -n +2 | sort -k1,1) \
+ <(cat ../input_files/synthetic.mate_1.bed | cut -f7 | sort | uniq -c | sort -k2nr | awk '{printf($2"\t"$1"\n")}')
+diff \
+ <(cat results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.salmon.pe/quant.genes.sf | cut -f1,5 | tail -n +2 | sort -k1,1) \
+ <(cat ../input_files/synthetic.mate_1.bed | cut -f7 | sort | uniq -c | sort -k2nr | awk '{printf($2"\t"$1"\n")}')
+
+
diff --git a/tests/test_scripts_prepare_inputs_table/test.sh b/tests/test_scripts_prepare_inputs_table/test.sh
index ebd9391..3c57024 100755
--- a/tests/test_scripts_prepare_inputs_table/test.sh
+++ b/tests/test_scripts_prepare_inputs_table/test.sh
@@ -35,7 +35,7 @@ python "../../scripts/prepare_inputs.py" \
# Check if dry run completes
snakemake \
- --snakefile="../../Snakefile" \
+ --snakefile="../../workflow/Snakefile" \
--configfile="config.yaml" \
--dryrun \
--verbose
diff --git a/Snakefile b/workflow/Snakefile
similarity index 96%
rename from Snakefile
rename to workflow/Snakefile
index c4c4e05..d46c511 100644
--- a/Snakefile
+++ b/workflow/Snakefile
@@ -100,8 +100,8 @@ def parse_rule_config(rule_config: dict, current_rule: str, immutable: Tuple[str
localrules: start, finish, rename_star_rpm_for_alfa, prepare_multiqc_config
# Include subworkflows
-include: os.path.join("workflow", "rules", "paired_end.snakefile.smk")
-include: os.path.join("workflow", "rules", "single_end.snakefile.smk")
+include: os.path.join("rules", "paired_end.snakefile.smk")
+include: os.path.join("rules", "single_end.snakefile.smk")
rule finish:
@@ -223,6 +223,9 @@ rule fastqc:
singularity:
"docker://quay.io/biocontainers/fastqc:0.11.9--hdfd78af_1"
+ conda:
+ os.path.join(workflow.basedir, "envs", "fastqc.yaml")
+
log:
stderr = os.path.join(
config["log_dir"],
@@ -304,6 +307,9 @@ rule create_index_star:
singularity:
"docker://quay.io/biocontainers/star:2.7.8a--h9ee0642_1"
+ conda:
+ os.path.join(workflow.basedir, "envs", "STAR.yaml")
+
threads: 12
log:
@@ -373,6 +379,9 @@ rule extract_transcriptome:
singularity:
"docker://quay.io/biocontainers/gffread:0.12.1--h2e03b76_1"
+ conda:
+ os.path.join(workflow.basedir, "envs", "gffread.yaml")
+
shell:
"(gffread \
-w {output.transcriptome} \
@@ -463,6 +472,9 @@ rule create_index_salmon:
singularity:
"docker://quay.io/biocontainers/salmon:1.4.0--h84f40af_1"
+
+ conda:
+ os.path.join(workflow.basedir, "envs", "salmon.yaml")
log:
stderr = os.path.join(
@@ -518,6 +530,9 @@ rule create_index_kallisto:
singularity:
"docker://quay.io/biocontainers/kallisto:0.46.2--h60f4f9f_2"
+ conda:
+ os.path.join(workflow.basedir, "envs", "kallisto.yaml")
+
log:
stderr = os.path.join(
config['log_dir'],
@@ -563,6 +578,9 @@ rule extract_transcripts_as_bed12:
singularity:
"docker://quay.io/biocontainers/zgtf:0.1.1--pyh5e36f6f_0"
+ conda:
+ os.path.join(workflow.basedir, "envs", "zgtf.yaml")
+
threads: 1
log:
@@ -611,6 +629,9 @@ rule index_genomic_alignment_samtools:
singularity:
"docker://quay.io/biocontainers/samtools:1.3.1--h1b8c3c0_8"
+ conda:
+ os.path.join(workflow.basedir, "envs", "samtools.yaml")
+
threads: 1
log:
@@ -700,6 +721,9 @@ rule calculate_TIN_scores:
singularity:
"docker://quay.io/biocontainers/tin-score-calculation:0.4--pyh5e36f6f_0"
+ conda:
+ os.path.join(workflow.basedir, "envs", "tin-score-calculation.yaml")
+
shell:
"(calculate-tin.py \
-i {input.bam} \
@@ -781,6 +805,9 @@ rule salmon_quantmerge_genes:
singularity:
"docker://quay.io/biocontainers/salmon:1.4.0--h84f40af_1"
+ conda:
+ os.path.join(workflow.basedir, "envs", "salmon.yaml")
+
shell:
"(salmon quantmerge \
--quants {params.salmon_in} \
@@ -864,6 +891,9 @@ rule salmon_quantmerge_transcripts:
singularity:
"docker://quay.io/biocontainers/salmon:1.4.0--h84f40af_1"
+ conda:
+ os.path.join(workflow.basedir, "envs", "salmon.yaml")
+
shell:
"(salmon quantmerge \
--quants {params.salmon_in} \
@@ -946,6 +976,9 @@ rule kallisto_merge_genes:
singularity:
"docker://quay.io/biocontainers/r-merge-kallisto:0.6--hdfd78af_0"
+ conda:
+ os.path.join(workflow.basedir, "envs", "r-merge-kallisto.yaml")
+
shell:
"(merge_kallisto.R \
--input {params.tables} \
@@ -1027,6 +1060,9 @@ rule kallisto_merge_transcripts:
singularity:
"docker://quay.io/biocontainers/r-merge-kallisto:0.6--hdfd78af_0"
+ conda:
+ os.path.join(workflow.basedir, "envs", "r-merge-kallisto.yaml")
+
shell:
"(merge_kallisto.R \
--input {params.tables} \
@@ -1074,6 +1110,9 @@ rule pca_salmon:
singularity:
"docker://quay.io/biocontainers/zpca:0.8.3.post1--pyh5e36f6f_0"
+ conda:
+ os.path.join(workflow.basedir, "envs", "zpca.yaml")
+
shell:
"(zpca-tpm \
--tpm {input.tpm} \
@@ -1120,6 +1159,9 @@ rule pca_kallisto:
singularity:
"docker://quay.io/biocontainers/zpca:0.8.3.post1--pyh5e36f6f_0"
+ conda:
+ os.path.join(workflow.basedir, "envs", "zpca.yaml")
+
shell:
"(zpca-tpm \
--tpm {input.tpm} \
@@ -1210,6 +1252,9 @@ rule star_rpm:
singularity:
"docker://quay.io/biocontainers/star:2.7.8a--h9ee0642_1"
+ conda:
+ os.path.join(workflow.basedir, "envs", "STAR.yaml")
+
log:
stderr = os.path.join(
config["log_dir"],
@@ -1356,6 +1401,9 @@ rule generate_alfa_index:
singularity:
"docker://quay.io/biocontainers/alfa:1.1.1--pyh5e36f6f_0"
+ conda:
+ os.path.join(workflow.basedir, "envs", "alfa.yaml")
+
log:
os.path.join(
config["log_dir"],
@@ -1459,6 +1507,9 @@ rule alfa_qc:
singularity:
"docker://quay.io/biocontainers/alfa:1.1.1--pyh5e36f6f_0"
+ conda:
+ os.path.join(workflow.basedir, "envs", "alfa.yaml")
+
log:
os.path.join(
config["log_dir"],
@@ -1484,7 +1535,6 @@ rule prepare_multiqc_config:
input:
script = os.path.join(
workflow.basedir,
- "workflow",
"scripts",
"zarp_multiqc_config.py")
@@ -1632,6 +1682,9 @@ rule multiqc_report:
singularity:
"docker://quay.io/biocontainers/zavolan-multiqc-plugins:1.3--pyh5e36f6f_0"
+ conda:
+ os.path.join(workflow.basedir, "envs", "zavolan-multiqc-plugins.yaml")
+
shell:
"(multiqc \
--outdir {output.multiqc_report} \
@@ -1676,6 +1729,9 @@ rule sort_bed_4_big:
singularity:
"docker://quay.io/biocontainers/bedtools:2.27.1--h9a82719_5"
+ conda:
+ os.path.join(workflow.basedir, "envs", "bedtools.yaml")
+
log:
stderr = os.path.join(
config["log_dir"],
@@ -1736,6 +1792,9 @@ rule prepare_bigWig:
singularity:
"docker://quay.io/biocontainers/ucsc-bedgraphtobigwig:377--h0b8a92a_2"
+ conda:
+ os.path.join(workflow.basedir, "envs", "ucsc-bedgraphtobigwig.yaml")
+
log:
stderr = os.path.join(
config["log_dir"],
diff --git a/workflow/envs/STAR.yaml b/workflow/envs/STAR.yaml
new file mode 100644
index 0000000..4c4b622
--- /dev/null
+++ b/workflow/envs/STAR.yaml
@@ -0,0 +1,7 @@
+---
+channels:
+ - conda-forge
+ - bioconda
+dependencies:
+ - STAR=2.7.8a
+...
diff --git a/workflow/envs/alfa.yaml b/workflow/envs/alfa.yaml
new file mode 100644
index 0000000..5f444fb
--- /dev/null
+++ b/workflow/envs/alfa.yaml
@@ -0,0 +1,7 @@
+---
+channels:
+ - conda-forge
+ - bioconda
+dependencies:
+ - alfa=1.1.1
+...
diff --git a/workflow/envs/bedtools.yaml b/workflow/envs/bedtools.yaml
new file mode 100644
index 0000000..2d40771
--- /dev/null
+++ b/workflow/envs/bedtools.yaml
@@ -0,0 +1,7 @@
+---
+channels:
+ - conda-forge
+ - bioconda
+dependencies:
+ - bedtools=2.27.1
+...
diff --git a/workflow/envs/cutadapt.yaml b/workflow/envs/cutadapt.yaml
new file mode 100644
index 0000000..064d302
--- /dev/null
+++ b/workflow/envs/cutadapt.yaml
@@ -0,0 +1,7 @@
+---
+channels:
+ - conda-forge
+ - bioconda
+dependencies:
+ - cutadapt=3.4
+...
diff --git a/workflow/envs/fastqc.yaml b/workflow/envs/fastqc.yaml
new file mode 100644
index 0000000..a5d96ff
--- /dev/null
+++ b/workflow/envs/fastqc.yaml
@@ -0,0 +1,7 @@
+---
+channels:
+ - conda-forge
+ - bioconda
+dependencies:
+ - fastqc=0.11.9
+...
diff --git a/workflow/envs/gffread.yaml b/workflow/envs/gffread.yaml
new file mode 100644
index 0000000..3b1399c
--- /dev/null
+++ b/workflow/envs/gffread.yaml
@@ -0,0 +1,7 @@
+---
+channels:
+ - conda-forge
+ - bioconda
+dependencies:
+ - gffread=0.12.1
+...
diff --git a/workflow/envs/kallisto.yaml b/workflow/envs/kallisto.yaml
new file mode 100644
index 0000000..977d1cd
--- /dev/null
+++ b/workflow/envs/kallisto.yaml
@@ -0,0 +1,7 @@
+---
+channels:
+ - conda-forge
+ - bioconda
+dependencies:
+ - kallisto=0.46.2
+...
diff --git a/workflow/envs/r-merge-kallisto.yaml b/workflow/envs/r-merge-kallisto.yaml
new file mode 100644
index 0000000..b069945
--- /dev/null
+++ b/workflow/envs/r-merge-kallisto.yaml
@@ -0,0 +1,7 @@
+---
+channels:
+ - conda-forge
+ - bioconda
+dependencies:
+ - r-merge-kallisto=0.6
+...
diff --git a/workflow/envs/salmon.yaml b/workflow/envs/salmon.yaml
new file mode 100644
index 0000000..9db5f9d
--- /dev/null
+++ b/workflow/envs/salmon.yaml
@@ -0,0 +1,7 @@
+---
+channels:
+ - conda-forge
+ - bioconda
+dependencies:
+ - salmon=1.4.0
+...
diff --git a/workflow/envs/samtools.yaml b/workflow/envs/samtools.yaml
new file mode 100644
index 0000000..0a515aa
--- /dev/null
+++ b/workflow/envs/samtools.yaml
@@ -0,0 +1,7 @@
+---
+channels:
+ - conda-forge
+ - bioconda
+dependencies:
+ - samtools=1.3.1
+...
diff --git a/workflow/envs/tin-score-calculation.yaml b/workflow/envs/tin-score-calculation.yaml
new file mode 100644
index 0000000..3cf610d
--- /dev/null
+++ b/workflow/envs/tin-score-calculation.yaml
@@ -0,0 +1,7 @@
+---
+channels:
+ - conda-forge
+ - bioconda
+dependencies:
+ - tin-score-calculation=0.4
+...
diff --git a/workflow/envs/ucsc-bedgraphtobigwig.yaml b/workflow/envs/ucsc-bedgraphtobigwig.yaml
new file mode 100644
index 0000000..7b79a3a
--- /dev/null
+++ b/workflow/envs/ucsc-bedgraphtobigwig.yaml
@@ -0,0 +1,7 @@
+---
+channels:
+ - conda-forge
+ - bioconda
+dependencies:
+ - ucsc-bedgraphtobigwig=377
+...
diff --git a/workflow/envs/zavolan-multiqc-plugins.yaml b/workflow/envs/zavolan-multiqc-plugins.yaml
new file mode 100644
index 0000000..4d11f50
--- /dev/null
+++ b/workflow/envs/zavolan-multiqc-plugins.yaml
@@ -0,0 +1,7 @@
+---
+channels:
+ - conda-forge
+ - bioconda
+dependencies:
+ - zavolan-multiqc-plugins=1.3
+...
diff --git a/workflow/envs/zgtf.yaml b/workflow/envs/zgtf.yaml
new file mode 100644
index 0000000..9e71d51
--- /dev/null
+++ b/workflow/envs/zgtf.yaml
@@ -0,0 +1,7 @@
+---
+channels:
+ - conda-forge
+ - bioconda
+dependencies:
+ - zgtf=0.1.1
+...
diff --git a/workflow/envs/zpca.yaml b/workflow/envs/zpca.yaml
new file mode 100644
index 0000000..faa0597
--- /dev/null
+++ b/workflow/envs/zpca.yaml
@@ -0,0 +1,7 @@
+---
+channels:
+ - conda-forge
+ - bioconda
+dependencies:
+ - zpca=0.8.3.post1
+...
diff --git a/workflow/rules/paired_end.snakefile.smk b/workflow/rules/paired_end.snakefile.smk
index 0fc0d6b..37c5546 100644
--- a/workflow/rules/paired_end.snakefile.smk
+++ b/workflow/rules/paired_end.snakefile.smk
@@ -55,6 +55,9 @@ rule pe_remove_adapters_cutadapt:
singularity:
"docker://quay.io/biocontainers/cutadapt:3.4--py37h73a75cf_1"
+ conda:
+ os.path.join(workflow.basedir, "envs", "cutadapt.yaml")
+
threads: 8
log:
@@ -150,6 +153,9 @@ rule pe_remove_polya_cutadapt:
singularity:
"docker://quay.io/biocontainers/cutadapt:3.4--py37h73a75cf_1"
+ conda:
+ os.path.join(workflow.basedir, "envs", "cutadapt.yaml")
+
threads: 8
log:
@@ -281,6 +287,9 @@ rule pe_map_genome_star:
singularity:
"docker://quay.io/biocontainers/star:2.7.8a--h9ee0642_1"
+ conda:
+ os.path.join(workflow.basedir, "envs", "STAR.yaml")
+
threads: 12
log:
@@ -416,6 +425,9 @@ rule pe_quantification_salmon:
singularity:
"docker://quay.io/biocontainers/salmon:1.4.0--h84f40af_1"
+ conda:
+ os.path.join(workflow.basedir, "envs", "salmon.yaml")
+
shell:
"(salmon quant \
--libType {params.libType} \
@@ -500,6 +512,9 @@ rule pe_genome_quantification_kallisto:
singularity:
"docker://quay.io/biocontainers/kallisto:0.46.2--h60f4f9f_2"
+ conda:
+ os.path.join(workflow.basedir, "envs", "kallisto.yaml")
+
threads: 8
log:
diff --git a/workflow/rules/single_end.snakefile.smk b/workflow/rules/single_end.snakefile.smk
index c60cfb5..e270aba 100644
--- a/workflow/rules/single_end.snakefile.smk
+++ b/workflow/rules/single_end.snakefile.smk
@@ -45,6 +45,9 @@ rule remove_adapters_cutadapt:
singularity:
"docker://quay.io/biocontainers/cutadapt:3.4--py37h73a75cf_1"
+ conda:
+ os.path.join(workflow.basedir, "envs", "cutadapt.yaml")
+
threads: 8
log:
@@ -115,6 +118,9 @@ rule remove_polya_cutadapt:
singularity:
"docker://quay.io/biocontainers/cutadapt:3.4--py37h73a75cf_1"
+ conda:
+ os.path.join(workflow.basedir, "envs", "cutadapt.yaml")
+
threads: 8
log:
@@ -225,6 +231,9 @@ rule map_genome_star:
singularity:
"docker://quay.io/biocontainers/star:2.7.8a--h9ee0642_1"
+ conda:
+ os.path.join(workflow.basedir, "envs", "STAR.yaml")
+
threads: 12
log:
@@ -363,6 +372,9 @@ rule quantification_salmon:
singularity:
"docker://quay.io/biocontainers/salmon:1.4.0--h84f40af_1"
+ conda:
+ os.path.join(workflow.basedir, "envs", "salmon.yaml")
+
shell:
"(salmon quant \
--libType {params.libType} \
@@ -461,6 +473,9 @@ rule genome_quantification_kallisto:
singularity:
"docker://quay.io/biocontainers/kallisto:0.46.2--h60f4f9f_2"
+ conda:
+ os.path.join(workflow.basedir, "envs", "kallisto.yaml")
+
shell:
"(kallisto quant \
--single \
--
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