Merge branch 'alfa' into 'master'

Alfa integration

See merge request zavolan_group/pipelines/rnaseqpipeline!41

tests/test_alfa/results/star_indexes/homo_sapiens/75/STAR_index/chrNameLength.txt

+Chr1	1500

tests/test_alfa/test.sh

+#!/bin/bash
+
+# Tear down test environment
+cleanup () {
+    rc=$?
+    rm -rf .java/
+    rm -rf .snakemake/
+    rm -rf logs/
+    rm -rfv results/alfa_indexes/
+    rm -rfv results/*/*/ALFA/
+    rm -rfv results/*/*/STAR_coverage/
+    rm -rfv results/ALFA/
+    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_alfa.yaml" \
+    --cores=4 \
+    --printshellcmds \
+    --rerun-incomplete \
+    --use-singularity \
+    --singularity-args="--bind ${PWD}/../input_files" \
+    --verbose \
+    results/ALFA/ALFA_plots.Categories.pdf
+
+# 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"

tests/test_integration_workflow/expected_output.md5

@@ -87,3 +87,11 @@ ede14ac41c10067838f375106fce4852  results/single_end/synthetic_10_reads_mate_1_s
 ea91b4f85622561158bff2f7c9c312b3  results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/STAR_coverage/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Signal.Unique.str1.out.bg
 ede14ac41c10067838f375106fce4852  results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/STAR_coverage/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Signal.Unique.str2.out.bg
 3ce47cb1d62482c5d62337751d7e8552  results/transcriptome/homo_sapiens/transcriptome.fa
+6b44c507f0a1c9f7369db0bb1deef0fd  results/alfa_indexes/homo_sapiens/75/ALFA/sorted_genes.stranded.ALFA_index
+2caebc23faf78fdbbbdbb118d28bd6b5  results/alfa_indexes/homo_sapiens/75/ALFA/sorted_genes.unstranded.ALFA_index
+c1254a0bae19ac3ffc39f73099ffcf2b  results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/synthetic_10_reads_paired_synthetic_10_reads_paired.ALFA_feature_counts.tsv
+c266d31e0a2ad84975cb9de335891e64  results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/synthetic_10_reads_paired_synthetic_10_reads_paired_Signal.UniqueMultiple.out.minus.bg
+0139e75ddbfe6eb081c2c2d9b9108ab4  results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/synthetic_10_reads_paired_synthetic_10_reads_paired_Signal.UniqueMultiple.out.plus.bg
+a9fdb9b135132dda339b85346525c9c5  results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.ALFA_feature_counts.tsv
+ede14ac41c10067838f375106fce4852  results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Signal.UniqueMultiple.out.minus.bg
+ea91b4f85622561158bff2f7c9c312b3  results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Signal.UniqueMultiple.out.plus.bg
\ No newline at end of file

tests/test_scripts_labkey_to_snakemake_api/expected_output.md5

-ba5ae0649d1fb82d94f8d19481498ffd  config.yaml
-cb58e046242c2702038e6e21dbd0bdb4  samples.tsv
\ No newline at end of file
+b163e7b06bd9e0a71f2fd1fc4935fea9  config.yaml
+cb58e046242c2702038e6e21dbd0bdb4  samples.tsv

tests/test_scripts_labkey_to_snakemake_table/expected_output.md5

-ba5ae0649d1fb82d94f8d19481498ffd  config.yaml
+b163e7b06bd9e0a71f2fd1fc4935fea9  config.yaml
 cb58e046242c2702038e6e21dbd0bdb4  samples.tsv

workflow/rules/paired_end.snakefile.smk

@@ -413,4 +413,5 @@ rule pe_genome_quantification_kallisto:
         --pseudobam \
         {params.directionality} \
         {input.reads1} {input.reads2} > {output.pseudoalignment}) \
-        2> {log.stderr}"
\ No newline at end of file
+        2> {log.stderr}"
+

workflow/rules/single_end.snakefile.smk

@@ -369,4 +369,5 @@ rule genome_quantification_kallisto:
         --pseudobam \
         {params.directionality} \
         {input.reads} > {output.pseudoalignment};) \
-        2> {log.stderr}"
\ No newline at end of file
+        2> {log.stderr}"
+