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Add automatic shell detection if not provided in image/powderaverage #50

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merged 3 commits into from
Nov 22, 2024
Merged

Add automatic shell detection if not provided in image/powderaverage #50

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4d1384b
add automatic shell detection if not provided in powder average + add…
gagnonanthony Nov 22, 2024
9146c62
revert shell change, update version fetching
gagnonanthony Nov 22, 2024
6f5f32b
Merge branch 'main' into shelldetectionpwdavg
gagnonanthony Nov 22, 2024
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2 changes: 1 addition & 1 deletion modules/nf-neuro/image/powderaverage/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -21,7 +21,7 @@ process IMAGE_POWDERAVERAGE {
def prefix = task.ext.prefix ?: "${meta.id}"

def b0_thr = task.ext.b0_thr ? "--b0_thr ${task.ext.b0_thr}" : ''
def shells = task.ext.shells ? "--shells ${task.ext.shells}" : ''
def shells = task.ext.shells ? "--shells ${task.ext.shells}" : "--shells \$(cut -d ' ' --output-delimiter=\$'\\n' -f 1- $bval | awk -F' ' '{v=int(\$1)}{print v}' | uniq)"
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@AlexVCaron AlexVCaron Nov 22, 2024 •
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The scilpy script is doing this job itself, when no shell argument is supplied. It also controls for uneven bvalues, that is really hard to do in bash. Why do we need this ?

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I can't remember exactly why (I should have noted it somewhere), but this fix worked. I'll try to reproduce the error and see what happens. Let's wait for merging in the meantime!

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Well, I've tried to reproduce the error again, but it seems to run fine now. I reverted the change @AlexVCaron !

def shell_thr = task.ext.shell_thr ? "--shell_thr ${task.ext.shell_thr}" : ''

if ( mask ) args += "--mask ${mask}"
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8 changes: 5 additions & 3 deletions modules/nf-neuro/image/powderaverage/tests/main.nf.test
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Expand Up @@ -24,7 +24,9 @@ nextflow_process {
}
}

test("powderaverage - no mask") {
test("powderaverage - no mask and no shell") {

config "./nextflow_noshells.config"

when {
process {
Expand All @@ -49,9 +51,9 @@ nextflow_process {
}
}

test("powderaverage - with mask") {
test("powderaverage - with mask and shells") {

config "./nextflow.config"
config "./nextflow_shells.config"

when {
process {
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20 changes: 10 additions & 10 deletions modules/nf-neuro/image/powderaverage/tests/main.nf.test.snap
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@@ -1,5 +1,5 @@
{
"powderaverage - with mask": {
"powderaverage - with mask and shells": {
"content": [
{
"0": [
Expand Down Expand Up @@ -29,12 +29,12 @@
}
],
"meta": {
"nf-test": "0.9.0-rc1",
"nextflow": "24.04.3"
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-07-26T12:43:21.971071"
"timestamp": "2024-11-22T17:09:05.483883967"
},
"powderaverage - no mask": {
"powderaverage - no mask and no shell": {
"content": [
{
"0": [
Expand All @@ -43,7 +43,7 @@
"id": "test",
"single_end": false
},
"test_pwd_avg.nii.gz:md5,168d711e7b84fad327966ca3d49ede0f"
"test_pwd_avg.nii.gz:md5,274a0826747914aa457c5a5363abffe5"
]
],
"1": [
Expand All @@ -55,7 +55,7 @@
"id": "test",
"single_end": false
},
"test_pwd_avg.nii.gz:md5,168d711e7b84fad327966ca3d49ede0f"
"test_pwd_avg.nii.gz:md5,274a0826747914aa457c5a5363abffe5"
]
],
"versions": [
Expand All @@ -64,9 +64,9 @@
}
],
"meta": {
"nf-test": "0.9.0-rc1",
"nextflow": "24.04.3"
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-07-25T14:32:47.643306"
"timestamp": "2024-11-22T17:09:00.254000809"
}
}
6 changes: 6 additions & 0 deletions modules/nf-neuro/image/powderaverage/tests/nextflow_noshells.config
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Original file line number Diff line number Diff line change
@@ -0,0 +1,6 @@
process {
withName: "IMAGE_POWDERAVERAGE" {
ext.b0_thr = 50
ext.shell_thr = 50
}
}
0 ...image/powderaverage/tests/nextflow.config → ...owderaverage/tests/nextflow_shells.config
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