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New nf-core role to pull methylseq, rnaseq, atacseq etc and other changes #332

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Feb 17, 2020
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141b42f
Add nf-core role
Dec 6, 2019
6f1baa9
Moved rnaseq, methylseq, ampliseq, atacseq to nfcore and upgraded neu…
aanil Jan 21, 2020
dc62f3b
Updated install.yml with nf-core
aanil Jan 21, 2020
114e370
Incorporate past changes
aanil Jan 21, 2020
858b02f
Update ngi reports and statusdb versions
aanil Jan 23, 2020
e243fba
Update sarek role to move to nf-core
aanil Jan 24, 2020
96eeeea
Revert "Update sarek role to move to nf-core"
aanil Jan 24, 2020
b79ec05
Revert "Update ngi reports and statusdb versions"
aanil Jan 24, 2020
187094f
Revert "Incorporate past changes"
aanil Jan 24, 2020
141f7d1
Revert "Updated install.yml with nf-core"
aanil Jan 24, 2020
f606eb2
Adding back conflicting files
aanil Jan 24, 2020
52094ed
Adding changes to sarek, standalone scripts, taca, rnaseq, methylseq,…
aanil Jan 24, 2020
11517b0
Fix issues in new Sarek script and neutronstar
aanil Jan 27, 2020
9d06e12
Add supernova and minor changes
aanil Jan 30, 2020
485ac02
Syntax bug fix in neutronstar
aanil Jan 30, 2020
381e14e
Update with latest ngi_reports version
aanil Jan 31, 2020
94b086d
Updated neutronstar parameters
aanil Feb 4, 2020
1728f9c
Updated location for downloading multiqc reports on staging env
aanil Feb 5, 2020
38ed3cc
Add export_plots to multiqc config
aanil Feb 6, 2020
cac433e
Removed container lists in nf-core role
aanil Feb 13, 2020
8c0c660
Updated neutronstar to use common irma config plus removed custom con…
aanil Feb 13, 2020
5763420
Updated neutronstar to use profile uppmax
aanil Feb 13, 2020
fc35214
Updated nextflow version
aanil Feb 17, 2020
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Update sarek role to move to nf-core
  • Loading branch information
aanil committed Jan 24, 2020
commit e243fba2d7c3a3234c535e8ff7aa08cab7feb8fe
4 changes: 1 addition & 3 deletions host_vars/127.0.0.1/main.yml
Original file line number Diff line number Diff line change
Expand Up @@ -44,9 +44,7 @@ ngi_pipeline_db_sthlm: "{{ ngi_pipeline_sthlm_path }}/db/records_db_sthlm.sql"
piper_module_version: 1.5.1
gatk_bundle_b37: "/sw/data/uppnex/piper_references/2016-04-07/gatk_bundle/2.8/b37/"

sarek_repo: "https://github.com/SciLifeLab/sarek.git"
sarek_version: "2.3.FIX1"
sarek_tag: "2.3"
sarek_tag: "2.5.2"
sarek_dest: "{{ sw_path }}/sarek"
sarek_containers: "{{ ngi_containers }}/sarek"
sarek_irma_config: "{{ ngi_pipeline_conf }}/sarek_irma.config"
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21 changes: 11 additions & 10 deletions roles/sarek/defaults/main.yml
Original file line number Diff line number Diff line change
@@ -1,11 +1,12 @@
---
sarek_containers_repo: "docker://maxulysse"
sarek_containers_images:
- "sarek"
- "r-base"
- "runallelecount"
- "snpeff"
- "snpeffgrch37"
- "snpeffgrch38"
- "vepgrch37"
- "vepgrch38"
sarek_containers_repo: "docker://nfcore"
sarek_repo: "https://github.com/nf-core/sarek.git"
sarek_version: "2.5.2"
sarek_genome_specific_containers:
- sarekvep
- sareksnpeff
sarek_genomes:
- GRCh38
- GRCh37
- GRCm38
- CanFam3.1
32 changes: 22 additions & 10 deletions roles/sarek/tasks/main.yml
Original file line number Diff line number Diff line change
Expand Up @@ -9,25 +9,37 @@
- name: Create sarek containers folder and temp/cache for images
file: name="{{ item }}" state=directory mode=g+s
with_items:
- "{{ sarek_containers }}/singularity_cache"
- "{{ sarek_containers }}/singularity_temp"
- "sarek/singularity_cache"
- "sarek/singularity_temp"

- name: Pull sarek Singularity images
command: "singularity build {{ item }}-{{ sarek_tag }}.simg {{ sarek_containers_repo }}/{{ item }}:{{ sarek_tag }}"
- name: Pull sarek Singularity image
command: "singularity pull --name sarek-{{ sarek_version}}.simg {{ sarek_containers_repo }}/sarek:{{ sarek_version }}"
environment:
SINGULARITY_CACHEDIR: "{{ sarek_containers }}/singularity_cache"
SINGULARITY_TMPDIR: "{{ sarek_containers }}/singularity_temp"
SINGULARITY_CACHEDIR: "sarek/singularity_cache"
SINGULARITY_TMPDIR: "sarek/singularity_temp"
args:
chdir: "{{ sarek_containers }}"
creates: "{{ item }}-{{ sarek_tag }}.img"
with_items: "{{ sarek_containers_images }}"
creates: "sarek-{{ version }}.simg"
ignore_errors: true

- name: Pull sarekvep, sareksnpeff Singularity images
command: "singularity pull --name {{ item.0 }}-{{ sarek_version }}.{{ item.1 }}.simg {{ sarek_containers_repo }}/{{ item.0 }}:{{ sarek_version }}.{{ item.1 }}"
environment:
SINGULARITY_CACHEDIR: "sarek/singularity_cache"
SINGULARITY_TMPDIR: "sarek/singularity_temp"
args:
chdir: "{{ sarek_containers }}"
creates: "{{ item.0 }}-{{ sarek_version }}.{{ item.1 }}.simg"
with_nested:
- "{{ sarek_genome_specific_containers }}"
- "{{ sarek_genomes }}"
ignore_errors: true

- name: Remove sarek containers temp directories
file: name="{{ item }}" state=absent
with_items:
- "{{ sarek_containers }}/singularity_cache"
- "{{ sarek_containers }}/singularity_temp"
- "sarek/singularity_cache"
- "sarek/singularity_temp"

- name: Deploy irma-specific sarek config
copy:
Expand Down