Merge branch 'feature/conda-support' into 'dev'

Conda support in ZARP See merge request !89

Merge branch 'feature/conda-support' into 'dev'
53b95906 · BIOPZ-Gypas Foivos · 2ab716c0 · 10885dca · 53b95906 · 53b95906
Commit 53b95906 authored 3 years ago by BIOPZ-Gypas Foivos
--- 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

--- 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

--- 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 \

--- 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 \

--- 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"


--- 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"


--- a/tests/test_integration_workflow_with_conda/expected_output.files
+++ b/tests/test_integration_workflow_with_conda/expected_output.files
+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
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+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
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+results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/quant_kallisto/synthetic_10_reads_paired_synthetic_10_reads_paired.pe.kallisto.pseudo.sam
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+results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/fastqc/fq1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.fq1_fastqc/fastqc.fo
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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/unmapped_names.txt
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+results/alfa_indexes/homo_sapiens/75/ALFA/sorted_genes.unstranded.ALFA_index
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+results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/Unique/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.ALFA_feature_counts.tsv
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+results/summary_kallisto/genes_tpm.tsv
\ No newline at end of file
--- a/tests/test_integration_workflow_with_conda/expected_output.md5
+++ b/tests/test_integration_workflow_with_conda/expected_output.md5
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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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+00dda17b3c3983873d1474e9a758d6e6  results/star_indexes/homo_sapiens/75/STAR_index/Genome
+c0d91c3af633d9439bfd0160d11efe4d  results/star_indexes/homo_sapiens/75/STAR_index/SA
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--- a/tests/test_integration_workflow_with_conda/test.local.sh
+++ b/tests/test_integration_workflow_with_conda/test.local.sh
+#!/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"$1"\n")}')
+
--- a/tests/test_integration_workflow_with_conda/test.slurm.sh
+++ b/tests/test_integration_workflow_with_conda/test.slurm.sh
+#!/bin/bash
+
+# Tear down test environment
+cleanup () {
+    rc=$?
+    # 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")}')
+
+
--- 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

--- a/Snakefile
+++ b/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"],

--- a/workflow/envs/STAR.yaml
+++ b/workflow/envs/STAR.yaml
+---
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - STAR=2.7.8a
+...
--- a/workflow/envs/alfa.yaml
+++ b/workflow/envs/alfa.yaml
+---
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - alfa=1.1.1
+...
--- a/workflow/envs/bedtools.yaml
+++ b/workflow/envs/bedtools.yaml
+---
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bedtools=2.27.1
+...
--- a/workflow/envs/cutadapt.yaml
+++ b/workflow/envs/cutadapt.yaml
+---
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - cutadapt=3.4
+...
--- a/workflow/envs/fastqc.yaml
+++ b/workflow/envs/fastqc.yaml
+---
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - fastqc=0.11.9
+...
--- a/workflow/envs/gffread.yaml
+++ b/workflow/envs/gffread.yaml
+---
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - gffread=0.12.1
+...
--- a/workflow/envs/kallisto.yaml
+++ b/workflow/envs/kallisto.yaml
+---
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - kallisto=0.46.2
+...
--- a/workflow/envs/r-merge-kallisto.yaml
+++ b/workflow/envs/r-merge-kallisto.yaml
+---
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - r-merge-kallisto=0.6
+...