Commit c6bdcbee authored by Sander Bollen's avatar Sander Bollen
Browse files

Merge branch 'licensing' into 'master'

Licensing

See merge request !10
parents 5096e6d9 0bb20d61
Pipeline #2413 passed with stage
in 1 minute and 36 seconds
......@@ -7,7 +7,11 @@ before_script:
test_sanities:
script:
- py.test --tag sanity
tags:
- docker
test_dry_run:
script:
- py.test --tag dry-run
tags:
- docker
This diff is collapsed.
......@@ -278,4 +278,9 @@ digraph snakemake_dag {
28 -> 27 [color="red"]
24 -> 28 [color="red"]
}
```
\ No newline at end of file
```
LICENSE
=======
AGPL-3.0
\ No newline at end of file
# hutspot - a DNAseq variant calling pipeline
# Copyright (C) 2017-2019, Sander Bollen, Leiden University Medical Center
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU Affero General Public License for more details.
#
# You should have received a copy of the GNU Affero General Public License
# along with this program. If not, see <https://www.gnu.org/licenses/>.
"""
Main Snakefile for the pipeline.
:copyright: (c) 2017-2019 Sander Bollen
:copyright: (c) 2017-2019 Leiden University Medical Center
:license: AGPL-3.0
"""
import json
from functools import partial
from os.path import join, basename
......
# hutspot - a DNAseq variant calling pipeline
# Copyright (C) 2017-2019, Sander Bollen, Leiden University Medical Center
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU Affero General Public License for more details.
#
# You should have received a copy of the GNU Affero General Public License
# along with this program. If not, see <https://www.gnu.org/licenses/>.
"""
collect_stats.py
~~~~~~~~~~~~~~~~
:copyright: (c) 2017-2019 Sander Bollen
:copyright: (c) 2017-2019 Leiden University Medical Center
:license: AGPL-3.0
"""
import click
import json
......@@ -116,4 +139,4 @@ def main(sample_name, pre_qc_fastq, post_qc_fastq, mapped_num, mapped_basenum,
if __name__ == "__main__":
main()
\ No newline at end of file
main()
# hutspot - a DNAseq variant calling pipeline
# Copyright (C) 2017-2019, Sander Bollen, Leiden University Medical Center
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU Affero General Public License for more details.
#
# You should have received a copy of the GNU Affero General Public License
# along with this program. If not, see <https://www.gnu.org/licenses/>.
"""
fastq-count.py
Pythonic equivalent to https://github.com/sndrtj/fastq-count
:copyright: (c) 2017-2019 Sander Bollen
:copyright: (c) 2017-2019 Leiden University Medical Center
:license: AGPL-3.0
"""
import click
import gzip
......@@ -111,4 +130,4 @@ def main(r1, r2):
if __name__ == "__main__":
main()
\ No newline at end of file
main()
# hutspot - a DNAseq variant calling pipeline
# Copyright (C) 2017-2019, Sander Bollen, Leiden University Medical Center
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU Affero General Public License for more details.
#
# You should have received a copy of the GNU Affero General Public License
# along with this program. If not, see <https://www.gnu.org/licenses/>.
"""
fastqc_stats.py
~~~~~~~~~~~~~~~
:copyright: (c) 2017-2019 Sander Bollen
:copyright: (c) 2017-2019 Leiden University Medical Center
:license: AGPL-3.0
"""
import argparse
import json
from pathlib import Path
......
# hutspot - a DNAseq variant calling pipeline
# Copyright (C) 2017-2019, Sander Bollen, Leiden University Medical Center
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU Affero General Public License for more details.
#
# You should have received a copy of the GNU Affero General Public License
# along with this program. If not, see <https://www.gnu.org/licenses/>.
"""
collect_stats.py
~~~~~~~~~~~~~~~~
:copyright: (c) 2017-2019 Sander Bollen
:copyright: (c) 2017-2019 Leiden University Medical Center
:license: AGPL-3.0
"""
import click
import json
......@@ -27,4 +51,4 @@ def main(vcfstats, collectstats):
if __name__ == "__main__":
main()
\ No newline at end of file
main()
#!/usr/bin/env bash
# hutspot - a DNAseq variant calling pipeline
# Copyright (C) 2017-2019, Sander Bollen, Leiden University Medical Center
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU Affero General Public License for more details.
#
# You should have received a copy of the GNU Affero General Public License
# along with this program. If not, see <https://www.gnu.org/licenses/>.
set -eu
set -o pipefail
......
#!/usr/bin/env bash
# hutspot - a DNAseq variant calling pipeline
# Copyright (C) 2017-2019, Sander Bollen, Leiden University Medical Center
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU Affero General Public License for more details.
#
# You should have received a copy of the GNU Affero General Public License
# along with this program. If not, see <https://www.gnu.org/licenses/>.
set -ex
set -o pipefail
......
# hutspot - a DNAseq variant calling pipeline
# Copyright (C) 2017-2019, Sander Bollen, Leiden University Medical Center
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU Affero General Public License for more details.
#
# You should have received a copy of the GNU Affero General Public License
# along with this program. If not, see <https://www.gnu.org/licenses/>.
"""
stats_to_tsv.py
~~~~~~~~~~~~~~~
:copyright: (c) 2017-2019 Sander Bollen
:copyright: (c) 2017-2019 Leiden University Medical Center
:license: AGPL-3.0
"""
import argparse
import json
......@@ -83,4 +106,4 @@ if __name__ == "__main__":
vals.append(sd[k])
else:
vals.append("NA")
print("\t".join(map(str, vals)))
\ No newline at end of file
print("\t".join(map(str, vals)))
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