diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 00dd3edfb91c82df4ecb952541abd0853d2d05f9..bd07e113ad5698f29ad0dd5f8a0af7a79d98fbb0 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 628833d3d860c6bd9341d94278770446c7631cb0..68a667e95924547abe048f850a158c8118777cfc 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 1c954dd3f80399aec892d7ab90b9ac75fd104063..87b5dad5c96199efcd5a40b0a9c03c03dde5b632 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 287e08d9d4831c79c0bff172f36653dd2012ca66..4e53450f53c781124ca7f617b23324f69623bce2 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 69b179dfa7d3d05c49b615261db891c93a416ad6..201c4cabafdca42fc4ff55ddf6d72419f6bd03ef 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 fd45fa49fe29f11f480e19ca38860a54f1ef5edc..48b95e8150b6e3da3b373627d60d6396091672ce 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 0000000000000000000000000000000000000000..a9026e6abe1da853ccee4e74f395d5a441de8cbf
--- /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
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+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
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+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
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+results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/bigWig/Unique/synthetic_10_reads_paired_synthetic_10_reads_paired_Unique_minus.bw
+results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/bigWig/Unique/synthetic_10_reads_paired_synthetic_10_reads_paired_Unique_plus.bw
+results/multiqc_summary/multiqc_data/multiqc_fastqc.txt
+results/multiqc_summary/multiqc_data/multiqc_cutadapt.txt
+results/multiqc_summary/multiqc_data/multiqc_cutadapt_1.txt
+results/multiqc_summary/multiqc_data/multiqc_star.txt
+results/multiqc_summary/multiqc_data/multiqc_kallisto.txt
+results/multiqc_summary/multiqc_data/multiqc_general_stats.txt
+results/summary_kallisto/tx2geneID.tsv
+results/summary_kallisto/genes_counts.tsv
+results/summary_kallisto/transcripts_counts.tsv
+results/summary_kallisto/transcripts_tpm.tsv
+results/summary_kallisto/genes_tpm.tsv
\ 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 0000000000000000000000000000000000000000..266f992944fb3e19dd0b0941d852c0e18f7a99f0
--- /dev/null
+++ b/tests/test_integration_workflow_with_conda/expected_output.md5
@@ -0,0 +1,96 @@
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+51b5292e3a874119c0e1aa566e95d70c results/salmon_indexes/homo_sapiens/31/salmon.idx/duplicate_clusters.tsv
+4e10114bb8f9096d594776181424a302 results/salmon_indexes/homo_sapiens/31/salmon.idx/info.json
+dee7cdc194d5d0617552b7a3b5ad8dfb results/star_indexes/homo_sapiens/75/STAR_index/chrLength.txt
+8e2e96e2d6b7f29940ad5de40662b7cb results/star_indexes/homo_sapiens/75/STAR_index/chrNameLength.txt
+d0826904b8afa45352906ad9591f2bfb results/star_indexes/homo_sapiens/75/STAR_index/chrName.txt
+8d3291e6bcdbe9902fbd7c887494173f results/star_indexes/homo_sapiens/75/STAR_index/chrStart.txt
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+bad9d837f9a988694cc7080ee6d2997a results/star_indexes/homo_sapiens/75/STAR_index/exonInfo.tab
+0c0b013fb8cbb8f3cb7a7bf92f3b1544 results/star_indexes/homo_sapiens/75/STAR_index/geneInfo.tab
+00dda17b3c3983873d1474e9a758d6e6 results/star_indexes/homo_sapiens/75/STAR_index/Genome
+c0d91c3af633d9439bfd0160d11efe4d results/star_indexes/homo_sapiens/75/STAR_index/SA
+a8dfc49713c053a8a1a2cc2527f15186 results/star_indexes/homo_sapiens/75/STAR_index/SAindex
+bae93882f9148a6c55816b733c32a3a2 results/star_indexes/homo_sapiens/75/STAR_index/sjdbInfo.txt
+875030141343fca11f0b5aa1a37e1b66 results/star_indexes/homo_sapiens/75/STAR_index/sjdbList.fromGTF.out.tab
+ea36f062eedc7f54ceffea2b635a25a8 results/star_indexes/homo_sapiens/75/STAR_index/sjdbList.out.tab
+65e794aa5096551254af18a678d02264 results/star_indexes/homo_sapiens/75/STAR_index/transcriptInfo.tab
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+500dd49da40b16799aba62aa5cf239ba results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.pe.remove_polya_mate1.fastq
+e90e31db1ce51d930645eb74ff70d21b results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.pe.remove_adapters_mate2.fastq
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+6946ba80af318b9c1052b264dc674a51 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq1/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1_fastqc/fastqc.fo
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+82c37e4cb9c1e167383d589ccb5c80b4 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq2/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2_fastqc/fastqc.fo
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+caf24c834f9f8aa31473c3d5826227ac 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
+909c316306050c8f7dfb9ad72dfe0334 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
+3f7d7acd0b42a4e3642f3cc8f81e7b8d 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
+5475f0266800b9febf00979b8dc561e6 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
+42462f1beeecb7820682284f7d5518cf 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
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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 0000000000000000000000000000000000000000..8a291088dff3cea7190bef09d05f74b12a3eb1bd
--- /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"$1"\n")}')
+
diff --git a/tests/test_integration_workflow_with_conda/test.slurm.sh b/tests/test_integration_workflow_with_conda/test.slurm.sh
new file mode 100755
index 0000000000000000000000000000000000000000..e4a7009040415e42ec4e991b28be31776f2c31bc
--- /dev/null
+++ b/tests/test_integration_workflow_with_conda/test.slurm.sh
@@ -0,0 +1,94 @@
+#!/bin/bash
+
+# Tear down test environment
+cleanup () {
+ rc=$?
+ # 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 ebd9391f2303cfe8e251c127d5748faa68ea7ba8..3c570241ebb83ad13da152e43a8f8666dc8b83d5 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 c4c4e05414cdeb1ce6c1dc66ef935c9a7b264380..d46c511b58c1152403ff0b05749cab4a796e34f8 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 0000000000000000000000000000000000000000..4c4b6226e38581604aaeba74e6cd1a81147b9aa7
--- /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 0000000000000000000000000000000000000000..5f444fb27c3324a02296af57cfc400df82460bd2
--- /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 0000000000000000000000000000000000000000..2d4077169c4777a1258bb444efd4e16b22510148
--- /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 0000000000000000000000000000000000000000..064d30234ed4b627aae8805b3d854b937480a926
--- /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 0000000000000000000000000000000000000000..a5d96ff8ce5b749a8139726cc70cc4595f42607b
--- /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 0000000000000000000000000000000000000000..3b1399ce9273598a648f01e581be76fe521fb8ae
--- /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 0000000000000000000000000000000000000000..977d1cd7473ee39b631cc3967f058e9a539ced74
--- /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 0000000000000000000000000000000000000000..b069945295b9240d5e0266d1fe91992481548629
--- /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 0000000000000000000000000000000000000000..9db5f9ddbafb883f88bb259bb9e67abaa7b5bb6b
--- /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 0000000000000000000000000000000000000000..0a515aa5869d727dcb5fbc40f82d0610b627045c
--- /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 0000000000000000000000000000000000000000..3cf610d59a0d2f1de130b2311014a8ebc1bd2c82
--- /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 0000000000000000000000000000000000000000..7b79a3ad81c0b87c046c8eb8c457c29db0ec7e5f
--- /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 0000000000000000000000000000000000000000..4d11f50a33d87893aa087b818c6ef4d268032c87
--- /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 0000000000000000000000000000000000000000..9e71d51f1977801cd7179eca8b25f2943f7bba0b
--- /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 0000000000000000000000000000000000000000..faa059705e2927977948ee20211cc8586e0b98fa
--- /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 0fc0d6b2ae014a385573942360e21b3b55087b85..37c55460935a5bc1c86716f3ad69efc96e7e5fde 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 c60cfb55f212cf74e465192844746e44ba49691b..e270aba84b8a70d69780aa5f31891b991dc8f54f 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 \