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LBMC
Hub
hic
Commits
3273c92c
Commit
3273c92c
authored
5 years ago
by
nservant
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update skip options
parent
f54bf1e1
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conf/test.config
+1
-1
1 addition, 1 deletion
conf/test.config
docs/usage.md
+12
-12
12 additions, 12 deletions
docs/usage.md
main.nf
+8
-8
8 additions, 8 deletions
main.nf
nextflow.config
+4
-4
4 additions, 4 deletions
nextflow.config
with
25 additions
and
25 deletions
conf/test.config
+
1
−
1
View file @
3273c92c
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@@ -29,5 +29,5 @@ params {
min_mapq
=
0
//
Options
skip
_c
ool
=
true
skip
C
ool
=
true
}
This diff is collapsed.
Click to expand it.
docs/usage.md
+
12
−
12
View file @
3273c92c
...
...
@@ -53,10 +53,10 @@
*
[
`--saveAlignedIntermediates`
](
#--saveAlignedIntermediates
)
*
[
`--saveInteractionBAM`
](
#--saveInteractionBAM
)
*
[
Skip options
](
#skip-options
)
*
[
--skip
_m
aps
](
#--skip
_m
aps
)
*
[
--skip
_i
ce
](
#--skip
_i
ce
)
*
[
--skip
_c
ool
](
#--skip
_c
ool
)
*
[
--skip
_m
ulti
qc
](
#--skip
_m
ulti
qc
)
*
[
--skip
M
aps
](
#--skip
M
aps
)
*
[
--skip
I
ce
](
#--skip
I
ce
)
*
[
--skip
C
ool
](
#--skip
C
ool
)
*
[
--skip
M
ulti
QC
](
#--skip
M
ulti
QC
)
*
[
Job resources
](
#job-resources
)
*
[
Automatic resubmission
](
#automatic-resubmission
)
*
[
Custom resource requests
](
#custom-resource-requests
)
...
...
@@ -561,38 +561,38 @@ dangling end, self-circle, etc.) and its tags.
## Skip options
### `--skip
_m
aps`
### `--skip
M
aps`
If defined, the workflow stops with the list of valid interactions, and the
genome-wide maps are not built. Usefult for capture-C analysis. Default: false
```
bash
--skip
_m
aps
--skip
M
aps
```
### `--skip
_i
ce`
### `--skip
I
ce`
If defined, the ICE normalization is not run on the raw contact maps.
Default: false
```
bash
--skip
_i
ce
--skip
I
ce
```
### `--skip
_c
ool`
### `--skip
C
ool`
If defined, cooler files are not generated. Default: false
```
bash
--skip
_c
ool
--skip
C
ool
```
### `--skip
_m
ulti
qc
`
### `--skip
M
ulti
QC
`
If defined, the MultiQC report is not generated. Default: false
```
bash
--skip
_m
ulti
qc
--skip
M
ulti
QC
```
## Job resources
...
...
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main.nf
+
8
−
8
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3273c92c
...
...
@@ -64,10 +64,10 @@ def helpMessage() {
Workflow
--skip
_m
aps Skip generation of contact maps. Useful for capture-C. Default: False
--skip
_i
ce Skip ICE normalization. Default: False
--skip
_c
ool Skip generation of cool files. Default: False
--skip
_m
ultiQC Skip MultiQC. Default: False
--skip
M
aps Skip generation of contact maps. Useful for capture-C. Default: False
--skip
I
ce Skip ICE normalization. Default: False
--skip
C
ool Skip generation of cool files. Default: False
--skip
M
ultiQC Skip MultiQC. Default: False
Other
--splitFastq Size of read chuncks to use to speed up the workflow. Default: None
...
...
@@ -734,7 +734,7 @@ process build_contact_maps{
publishDir "${params.outdir}/hic_results/matrix/raw", mode: 'copy'
when:
!params.skip
_m
aps
!params.skip
M
aps
input:
set val(sample), file(vpairs), val(mres) from all_valid_pairs.combine(map_res)
...
...
@@ -759,7 +759,7 @@ process run_ice{
publishDir "${params.outdir}/hic_results/matrix/iced", mode: 'copy'
when:
!params.skip
_m
aps && !params.skip
_i
ce
!params.skip
M
aps && !params.skip
I
ce
input:
file(rmaps) from raw_maps
...
...
@@ -787,7 +787,7 @@ process generate_cool{
publishDir "${params.outdir}/export/cool", mode: 'copy'
when:
!params.skip
_c
ool
!params.skip
C
ool
input:
set val(sample), file(vpairs) from all_valid_pairs_4cool
...
...
@@ -810,7 +810,7 @@ process multiqc {
publishDir "${params.outdir}/MultiQC", mode: 'copy'
when:
!params.skip
_m
ulti
qc
!params.skip
M
ulti
QC
input:
file multiqc_config from ch_multiqc_config
...
...
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nextflow.config
+
4
−
4
View file @
3273c92c
...
...
@@ -16,10 +16,10 @@ params {
readPaths
=
false
chromosome_size
=
false
restriction_fragments
=
false
skip
_m
aps
=
false
skip
_i
ce
=
false
skip
_c
ool
=
false
skip
_m
ulti
qc
=
false
skip
M
aps
=
false
skip
I
ce
=
false
skip
C
ool
=
false
skip
M
ulti
QC
=
false
dnase
=
false
//
Boilerplate
options
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