Skip to content

Commit 414efe6

Browse files
davidebolo1993davidebolo1993
authored
Merge pull request #9 from davidebolo1993/test_add_conda
Test add conda
2 parents d93666f + f0af9d0 commit 414efe6

26 files changed

+189
-61
lines changed

Diff for: ‎Dockerfile

+1-2
Original file line numberDiff line numberDiff line change
@@ -68,8 +68,7 @@ RUN pip3 install numpy \
6868
pandas \
6969
matplotlib \
7070
scikit-learn \
71-
scipy \
72-
pyfaidx
71+
scipy
7372

7473
#ln python to python3 -not used right now but, who knows?
7574
RUN ln -s /usr/bin/python3 /usr/bin/python

Diff for: ‎cosigt_smk/workflow/Snakefile

-1
Original file line numberDiff line numberDiff line change
@@ -12,7 +12,6 @@ include: 'rules/wfmash.smk'
1212
include: 'rules/impg.smk'
1313
include: 'rules/bedtools.smk'
1414
include: 'rules/samtools.smk'
15-
include: 'rules/faidx.smk'
1615
include: 'rules/pggb.smk'
1716
include: 'rules/odgi.smk'
1817
include: 'rules/bwa-mem2.smk'

Diff for: ‎cosigt_smk/workflow/envs/bedtools.yaml

+5
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,5 @@
1+
channels:
2+
- conda-forge
3+
- bioconda
4+
dependencies:
5+
- bedtools=2.31.1

Diff for: ‎cosigt_smk/workflow/envs/bwa-mem2.yaml

+6
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,6 @@
1+
channels:
2+
- conda-forge
3+
- bioconda
4+
dependencies:
5+
- bwa-mem2=2.2.1
6+
- samtools=1.21

Diff for: ‎cosigt_smk/workflow/envs/cluster.yaml

+9
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,9 @@
1+
channels:
2+
- conda-forge
3+
- bioconda
4+
dependencies:
5+
- scikit-learn=1.5.2
6+
- matplotlib=3.9.2
7+
- scipy=1.14.1
8+
- pandas=2.2.3
9+
- numpy=2.1.2

Diff for: ‎cosigt_smk/workflow/envs/cosigt.yaml

+5
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,5 @@
1+
channels:
2+
- conda-forge
3+
- bioconda
4+
dependencies:
5+
- cosigt

Diff for: ‎cosigt_smk/workflow/envs/gafpack.yaml

+5
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,5 @@
1+
channels:
2+
- conda-forge
3+
- bioconda
4+
dependencies:
5+
- gafpack

Diff for: ‎cosigt_smk/workflow/envs/gfainject.yaml

+5
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,5 @@
1+
channels:
2+
- conda-forge
3+
- bioconda
4+
dependencies:
5+
- gfainject=0.1.0

Diff for: ‎cosigt_smk/workflow/envs/impg.yaml

+5
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,5 @@
1+
channels:
2+
- conda-forge
3+
- bioconda
4+
dependencies:
5+
- impg=0.2.1

Diff for: ‎cosigt_smk/workflow/envs/megadepth.yaml

+5
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,5 @@
1+
channels:
2+
- conda-forge
3+
- bioconda
4+
dependencies:
5+
- megadepth=1.2.0

Diff for: ‎cosigt_smk/workflow/envs/odgi.yaml

+5
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,5 @@
1+
channels:
2+
- conda-forge
3+
- bioconda
4+
dependencies:
5+
- odgi=0.8.6

Diff for: ‎cosigt_smk/workflow/envs/pggb.yaml

+5
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,5 @@
1+
channels:
2+
- conda-forge
3+
- bioconda
4+
dependencies:
5+
- pggb=0.6.0

Diff for: ‎cosigt_smk/workflow/envs/samtools.yaml

+5
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,5 @@
1+
channels:
2+
- conda-forge
3+
- bioconda
4+
dependencies:
5+
- samtools=1.21

Diff for: ‎cosigt_smk/workflow/envs/wfmash.yaml

+5
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,5 @@
1+
channels:
2+
- conda-forge
3+
- bioconda
4+
dependencies:
5+
- wfmash=0.15.0

Diff for: ‎cosigt_smk/workflow/rules/bedtools.smk

+2
Original file line numberDiff line numberDiff line change
@@ -13,6 +13,8 @@ rule bedtools_merge:
1313
time=lambda wildcards, attempt: attempt * config['default']['time']
1414
container:
1515
'docker://davidebolo1993/cosigt_workflow:latest'
16+
conda:
17+
'../envs/bedtools.yaml'
1618
benchmark:
1719
'benchmarks/{region}.bedtools_merge.benchmark.txt'
1820
params:

Diff for: ‎cosigt_smk/workflow/rules/bwa-mem2.smk

+4
Original file line numberDiff line numberDiff line change
@@ -13,6 +13,8 @@ rule bwamem2_index:
1313
time=lambda wildcards, attempt: attempt * config['bwa-mem2']['time']
1414
container:
1515
'docker://davidebolo1993/cosigt_workflow:latest'
16+
conda:
17+
'../envs/bwa-mem2.yaml'
1618
benchmark:
1719
'benchmarks/{region}.bwamem2_index.benchmark.txt'
1820
shell:
@@ -38,6 +40,8 @@ rule bwamem2_mem_samtools_sort:
3840
time=lambda wildcards, attempt: attempt * config['bwa-mem2']['time']
3941
container:
4042
'docker://davidebolo1993/cosigt_workflow:latest'
43+
conda:
44+
'../envs/bwa-mem2.yaml'
4145
benchmark:
4246
'benchmarks/{sample}.{region}.bwamem2_mem_samtools_sort.benchmark.txt'
4347
shell:

Diff for: ‎cosigt_smk/workflow/rules/cosigt.smk

+2
Original file line numberDiff line numberDiff line change
@@ -16,6 +16,8 @@ rule cosigt_genotype:
1616
time=lambda wildcards, attempt: attempt * config['default']['time']
1717
container:
1818
'docker://davidebolo1993/cosigt_workflow:latest'
19+
conda:
20+
'../envs/cosigt.yaml'
1921
params:
2022
prefix=config['output'] + '/cosigt/{sample}/{region}'
2123
benchmark:

Diff for: ‎cosigt_smk/workflow/rules/faidx.smk

-46
This file was deleted.

Diff for: ‎cosigt_smk/workflow/rules/gafpack.smk

+2
Original file line numberDiff line numberDiff line change
@@ -14,6 +14,8 @@ rule gafpack_coverage:
1414
time=lambda wildcards, attempt: attempt * config['default']['time']
1515
container:
1616
'docker://davidebolo1993/cosigt_workflow:latest'
17+
conda:
18+
'../envs/gafpack.yaml'
1719
benchmark:
1820
'benchmarks/{sample}.{region}.gafpack_coverage.benchmark.txt'
1921
shell:

Diff for: ‎cosigt_smk/workflow/rules/gfainject.smk

+2
Original file line numberDiff line numberDiff line change
@@ -14,6 +14,8 @@ rule gfainject_inject:
1414
time=lambda wildcards, attempt: attempt * config['default']['time']
1515
container:
1616
'docker://davidebolo1993/cosigt_workflow:latest'
17+
conda:
18+
'../envs/gfainject.yaml'
1719
benchmark:
1820
'benchmarks/{sample}.{region}.gfainject_inject.benchmark.txt'
1921
shell:

Diff for: ‎cosigt_smk/workflow/rules/impg.smk

+2
Original file line numberDiff line numberDiff line change
@@ -14,6 +14,8 @@ rule impg_project:
1414
time=lambda wildcards, attempt: attempt * config['default']['time']
1515
container:
1616
'docker://davidebolo1993/cosigt_workflow:latest'
17+
conda:
18+
'../envs/impg.yaml'
1719
benchmark:
1820
'benchmarks/{region}.impg_project.benchmark.txt'
1921
params:

Diff for: ‎cosigt_smk/workflow/rules/megadepth.smk

+2
Original file line numberDiff line numberDiff line change
@@ -13,6 +13,8 @@ rule megadepth_bam_to_bigwig:
1313
time=lambda wildcards, attempt: attempt * config['default']['time']
1414
container:
1515
'docker://davidebolo1993/cosigt_workflow:latest'
16+
conda:
17+
'../envs/megdepth.yaml'
1618
benchmark:
1719
'benchmarks/{sample}.{region}.megadepth_bam_to_bigwig.benchmark.txt'
1820
shell:

Diff for: ‎cosigt_smk/workflow/rules/odgi.smk

+19-7
Original file line numberDiff line numberDiff line change
@@ -13,6 +13,8 @@ rule odgi_chop:
1313
time=lambda wildcards, attempt: attempt * config['default']['time']
1414
container:
1515
'docker://pangenome/odgi:1726671973'
16+
conda:
17+
'../envs/odgi.yaml'
1618
benchmark:
1719
'benchmarks/{region}.odgi_chop.benchmark.txt'
1820
shell:
@@ -38,6 +40,8 @@ rule odgi_view:
3840
time=lambda wildcards, attempt: attempt * config['default']['time']
3941
container:
4042
'docker://pangenome/odgi:1726671973'
43+
conda:
44+
'../envs/odgi.yaml'
4145
benchmark:
4246
'benchmarks/{region}.odgi_view.benchmark.txt'
4347
shell:
@@ -62,6 +66,8 @@ rule odgi_paths_matrix:
6266
time=lambda wildcards, attempt: attempt * config['default']['time']
6367
container:
6468
'docker://pangenome/odgi:1726671973'
69+
conda:
70+
'../envs/odgi.yaml'
6571
benchmark:
6672
'benchmarks/{region}.odgi_paths_matrix.benchmark.txt'
6773
shell:
@@ -72,7 +78,6 @@ rule odgi_paths_matrix:
7278
cut -f 1,4- | gzip > {output}
7379
'''
7480

75-
7681
rule odgi_similarity:
7782
'''
7883
https://github.com/pangenome/odgi
@@ -88,6 +93,8 @@ rule odgi_similarity:
8893
time=lambda wildcards, attempt: attempt * config['default']['time']
8994
container:
9095
'docker://pangenome/odgi:1726671973'
96+
conda:
97+
'../envs/odgi.yaml'
9198
benchmark:
9299
'benchmarks/{region}.odgi_similarity.benchmark.txt'
93100
shell:
@@ -96,7 +103,6 @@ rule odgi_similarity:
96103
-i {input} > {output}
97104
'''
98105

99-
100106
rule make_clusters:
101107
'''
102108
https://github.com/davidebolo1993/cosigt
@@ -112,6 +118,8 @@ rule make_clusters:
112118
time=lambda wildcards, attempt: attempt * config['default']['time']
113119
container:
114120
'docker://davidebolo1993/cosigt_workflow:latest'
121+
conda:
122+
'../envs/cluster.yaml'
115123
benchmark:
116124
'benchmarks/{region}.make_clusters.benchmark.txt'
117125
params:
@@ -123,7 +131,6 @@ rule make_clusters:
123131
{params.prefix}
124132
'''
125133

126-
127134
#plot structures when using rule annotate
128135
rule odgi_procbed:
129136
'''
@@ -141,6 +148,8 @@ rule odgi_procbed:
141148
time=lambda wildcards, attempt: attempt * config['default']['time']
142149
container:
143150
'docker://pangenome/odgi:1726671973'
151+
conda:
152+
'../envs/odgi.yaml'
144153
benchmark:
145154
'benchmarks/{region}.odgi_procbed.benchmark.txt'
146155
shell:
@@ -150,7 +159,6 @@ rule odgi_procbed:
150159
-b {input.bed} > {output}
151160
'''
152161

153-
154162
rule annot_names:
155163
'''
156164
https://github.com/davidebolo1993/cosigt
@@ -188,6 +196,8 @@ rule odgi_inject:
188196
time=lambda wildcards, attempt: attempt * config['default']['time']
189197
container:
190198
'docker://pangenome/odgi:1726671973'
199+
conda:
200+
'../envs/odgi.yaml'
191201
benchmark:
192202
'benchmarks/{region}.odgi_inject.benchmark.txt'
193203
shell:
@@ -198,7 +208,6 @@ rule odgi_inject:
198208
-o {output}
199209
'''
200210

201-
202211
rule odgi_flip:
203212
'''
204213
https://github.com/pangenome/odgi
@@ -214,6 +223,8 @@ rule odgi_flip:
214223
time=lambda wildcards, attempt: attempt * config['default']['time']
215224
container:
216225
'docker://pangenome/odgi:1726671973'
226+
conda:
227+
'../envs/odgi.yaml'
217228
benchmark:
218229
'benchmarks/{region}.odgi_flip.benchmark.txt'
219230
shell:
@@ -223,7 +234,6 @@ rule odgi_flip:
223234
-o {output}
224235
'''
225236

226-
227237
rule odgi_untangle:
228238
'''
229239
https://github.com/pangenome/odgi
@@ -240,6 +250,8 @@ rule odgi_untangle:
240250
time=lambda wildcards, attempt: attempt * config['default']['time']
241251
container:
242252
'docker://pangenome/odgi:1726671973'
253+
conda:
254+
'../envs/odgi.yaml'
243255
benchmark:
244256
'benchmarks/{region}.odgi_untangle.benchmark.txt'
245257
shell:
@@ -249,4 +261,4 @@ rule odgi_untangle:
249261
-i {input.og} \
250262
-j 0.3 \
251263
-g > {output}
252-
'''
264+
'''

Diff for: ‎cosigt_smk/workflow/rules/pggb.smk

+3-1
Original file line numberDiff line numberDiff line change
@@ -3,7 +3,7 @@ rule pggb_construct:
33
https://github.com/pangenome/pggb
44
'''
55
input:
6-
fasta=rules.pyfaidx_extract.output,
6+
fasta=rules.samtools_faidx_extract.output,
77
index=rules.samtools_faidx_index.output
88
output:
99
config['output'] + '/pggb/{region}.og'
@@ -14,6 +14,8 @@ rule pggb_construct:
1414
time=lambda wildcards, attempt: attempt * config['pggb']['time']
1515
container:
1616
'docker://pangenome/pggb:latest'
17+
conda:
18+
'../envs/pggb.yaml'
1719
benchmark:
1820
'benchmarks/{region}.pggb_construct.benchmark.txt'
1921
params:

0 commit comments

Comments
 (0)