From 1e52fa5604db6ca59f353dbf3c9c18d12cad665d Mon Sep 17 00:00:00 2001
From: Alex Kanitz <alexander.kanitz@unibas.ch>
Date: Fri, 14 Feb 2020 17:47:54 +0100
Subject: [PATCH] repo follows recommended structure
---
.gitlab-ci.yml | 2 +-
snakemake/Snakefile => Snakefile | 4 ++--
{runs => config}/PUT_YOUR_WORKFLOW_RUN_CONFIGS_HERE | 0
tests/test_create_dag_image/test.sh | 4 ++--
.../config.yaml | 0
.../input_files/chr1-10000-20000.fa | 0
.../input_files/chr1-10000-20000.gtf | 0
.../input_files/chr1-10000-20000.transcripts.fa | 0
.../input_files/synthetic.mate_1.fastq.gz | Bin
.../input_files/synthetic.mate_2.fastq.gz | Bin
.../samples.tsv | 0
.../test.sh | 4 ++--
tests/test_integration_workflow/test.local.sh | 2 +-
tests/test_integration_workflow/test.slurm.sh | 2 +-
tests/test_scripts_labkey_to_snakemake/test.sh | 4 ++--
.../rules}/paired_end.snakefile.smk | 0
.../rules}/single_end.snakefile.smk | 0
17 files changed, 11 insertions(+), 11 deletions(-)
rename snakemake/Snakefile => Snakefile (97%)
rename {runs => config}/PUT_YOUR_WORKFLOW_RUN_CONFIGS_HERE (100%)
rename tests/{test_rule_graph => test_create_rule_graph}/config.yaml (100%)
rename tests/{test_rule_graph => test_create_rule_graph}/input_files/chr1-10000-20000.fa (100%)
rename tests/{test_rule_graph => test_create_rule_graph}/input_files/chr1-10000-20000.gtf (100%)
rename tests/{test_rule_graph => test_create_rule_graph}/input_files/chr1-10000-20000.transcripts.fa (100%)
rename tests/{test_rule_graph => test_create_rule_graph}/input_files/synthetic.mate_1.fastq.gz (100%)
rename tests/{test_rule_graph => test_create_rule_graph}/input_files/synthetic.mate_2.fastq.gz (100%)
rename tests/{test_rule_graph => test_create_rule_graph}/samples.tsv (100%)
rename tests/{test_rule_graph => test_create_rule_graph}/test.sh (78%)
rename {snakemake => workflow/rules}/paired_end.snakefile.smk (100%)
rename {snakemake => workflow/rules}/single_end.snakefile.smk (100%)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 7934c08..931b300 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -13,6 +13,6 @@ test:
- bash tests/test_scripts_labkey_to_snakemake/test.sh
# add integration tests here
- bash tests/test_create_dag_image/test.sh
- - bash tests/test_rule_graph/test.sh
+ - bash tests/test_create_rule_graph/test.sh
- bash tests/test_integration_workflow/test.local.sh
diff --git a/snakemake/Snakefile b/Snakefile
similarity index 97%
rename from snakemake/Snakefile
rename to Snakefile
index ba4bb99..c311cd0 100644
--- a/snakemake/Snakefile
+++ b/Snakefile
@@ -18,8 +18,8 @@ localrules: finish
# Execution dependend on sequencing mode
##################################################################################
-include: 'paired_end.snakefile.smk'
-include: 'single_end.snakefile.smk'
+include: os.path.join('workflow', 'rules', 'paired_end.snakefile.smk')
+include: os.path.join('workflow', 'rules', 'single_end.snakefile.smk')
#################################################################################
### Final rule
diff --git a/runs/PUT_YOUR_WORKFLOW_RUN_CONFIGS_HERE b/config/PUT_YOUR_WORKFLOW_RUN_CONFIGS_HERE
similarity index 100%
rename from runs/PUT_YOUR_WORKFLOW_RUN_CONFIGS_HERE
rename to config/PUT_YOUR_WORKFLOW_RUN_CONFIGS_HERE
diff --git a/tests/test_create_dag_image/test.sh b/tests/test_create_dag_image/test.sh
index 6043d63..c377a7e 100755
--- a/tests/test_create_dag_image/test.sh
+++ b/tests/test_create_dag_image/test.sh
@@ -1,7 +1,7 @@
#!/bin/bash
# Tear down test environment
-trap 'cd $user_dir' EXIT # quotes command is exected after script exits, regardless of exit status
+trap 'rm -rf .snakemake && cd $user_dir' EXIT # quotes command is exected after script exits, regardless of exit status
# Set up test environment
set -eo pipefail # ensures that script exits at first command that exits with non-zero status
@@ -13,7 +13,7 @@ cd $script_dir
# Run tests
snakemake \
- --snakefile="../../snakemake/Snakefile" \
+ --snakefile="../../Snakefile" \
--configfile="config.yaml" \
--dag \
--printshellcmds \
diff --git a/tests/test_rule_graph/config.yaml b/tests/test_create_rule_graph/config.yaml
similarity index 100%
rename from tests/test_rule_graph/config.yaml
rename to tests/test_create_rule_graph/config.yaml
diff --git a/tests/test_rule_graph/input_files/chr1-10000-20000.fa b/tests/test_create_rule_graph/input_files/chr1-10000-20000.fa
similarity index 100%
rename from tests/test_rule_graph/input_files/chr1-10000-20000.fa
rename to tests/test_create_rule_graph/input_files/chr1-10000-20000.fa
diff --git a/tests/test_rule_graph/input_files/chr1-10000-20000.gtf b/tests/test_create_rule_graph/input_files/chr1-10000-20000.gtf
similarity index 100%
rename from tests/test_rule_graph/input_files/chr1-10000-20000.gtf
rename to tests/test_create_rule_graph/input_files/chr1-10000-20000.gtf
diff --git a/tests/test_rule_graph/input_files/chr1-10000-20000.transcripts.fa b/tests/test_create_rule_graph/input_files/chr1-10000-20000.transcripts.fa
similarity index 100%
rename from tests/test_rule_graph/input_files/chr1-10000-20000.transcripts.fa
rename to tests/test_create_rule_graph/input_files/chr1-10000-20000.transcripts.fa
diff --git a/tests/test_rule_graph/input_files/synthetic.mate_1.fastq.gz b/tests/test_create_rule_graph/input_files/synthetic.mate_1.fastq.gz
similarity index 100%
rename from tests/test_rule_graph/input_files/synthetic.mate_1.fastq.gz
rename to tests/test_create_rule_graph/input_files/synthetic.mate_1.fastq.gz
diff --git a/tests/test_rule_graph/input_files/synthetic.mate_2.fastq.gz b/tests/test_create_rule_graph/input_files/synthetic.mate_2.fastq.gz
similarity index 100%
rename from tests/test_rule_graph/input_files/synthetic.mate_2.fastq.gz
rename to tests/test_create_rule_graph/input_files/synthetic.mate_2.fastq.gz
diff --git a/tests/test_rule_graph/samples.tsv b/tests/test_create_rule_graph/samples.tsv
similarity index 100%
rename from tests/test_rule_graph/samples.tsv
rename to tests/test_create_rule_graph/samples.tsv
diff --git a/tests/test_rule_graph/test.sh b/tests/test_create_rule_graph/test.sh
similarity index 78%
rename from tests/test_rule_graph/test.sh
rename to tests/test_create_rule_graph/test.sh
index d68df4f..b67a888 100755
--- a/tests/test_rule_graph/test.sh
+++ b/tests/test_create_rule_graph/test.sh
@@ -1,7 +1,7 @@
#!/bin/bash
# Tear down test environment
-trap 'cd $user_dir' EXIT # quotes command is exected after script exits, regardless of exit status
+trap 'rm -rf .snakemake && cd $user_dir' EXIT # quotes command is exected after script exits, regardless of exit status
# Set up test environment
set -eo pipefail # ensures that script exits at first command that exits with non-zero status
@@ -13,7 +13,7 @@ cd $script_dir
# Run tests
snakemake \
- --snakefile="../../snakemake/Snakefile" \
+ --snakefile="../../Snakefile" \
--configfile="config.yaml" \
--rulegraph \
--printshellcmds \
diff --git a/tests/test_integration_workflow/test.local.sh b/tests/test_integration_workflow/test.local.sh
index 4a5da25..a87ff58 100755
--- a/tests/test_integration_workflow/test.local.sh
+++ b/tests/test_integration_workflow/test.local.sh
@@ -14,7 +14,7 @@ mkdir -p logs/local_log
# Run tests
snakemake \
- --snakefile="../../snakemake/Snakefile" \
+ --snakefile="../../Snakefile" \
--configfile="config.yaml" \
--cores=4 \
--printshellcmds \
diff --git a/tests/test_integration_workflow/test.slurm.sh b/tests/test_integration_workflow/test.slurm.sh
index 2f2c9e7..246a1e5 100755
--- a/tests/test_integration_workflow/test.slurm.sh
+++ b/tests/test_integration_workflow/test.slurm.sh
@@ -15,7 +15,7 @@ mkdir -p logs/local_log
# Run tests
snakemake \
- --snakefile="../../snakemake/Snakefile" \
+ --snakefile="../../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" \
diff --git a/tests/test_scripts_labkey_to_snakemake/test.sh b/tests/test_scripts_labkey_to_snakemake/test.sh
index 27846cc..a62b53b 100755
--- a/tests/test_scripts_labkey_to_snakemake/test.sh
+++ b/tests/test_scripts_labkey_to_snakemake/test.sh
@@ -1,7 +1,7 @@
#!/bin/bash
# Tear down test environment
-trap 'rm config.yaml samples.tsv && cd $user_dir' EXIT # quotes command is exected after script exits, regardless of exit status
+trap 'rm -rf config.yaml samples.tsv .snakemake && cd $user_dir' EXIT # quotes command is exected after script exits, regardless of exit status
#
# Set up test environment
set -eo pipefail # ensures that script exits at first command that exits with non-zero status
@@ -25,7 +25,7 @@ python "../../scripts/labkey_to_snakemake.py" \
snakemake \
- --snakefile="../../snakemake/Snakefile" \
+ --snakefile="../../Snakefile" \
--configfile="config.yaml" \
--dryrun \
# --rulegraph \
diff --git a/snakemake/paired_end.snakefile.smk b/workflow/rules/paired_end.snakefile.smk
similarity index 100%
rename from snakemake/paired_end.snakefile.smk
rename to workflow/rules/paired_end.snakefile.smk
diff --git a/snakemake/single_end.snakefile.smk b/workflow/rules/single_end.snakefile.smk
similarity index 100%
rename from snakemake/single_end.snakefile.smk
rename to workflow/rules/single_end.snakefile.smk
--
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