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Remove .fromSamplesheet, but create an equivalent function samplesheetToList #3

Merged
merged 23 commits into from
Apr 18, 2024
Merged

Remove .fromSamplesheet, but create an equivalent function samplesheetToList #3

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4970b54
simple steps for the transition to an operator
nvnieuwk Mar 20, 2024
18ae17c
Merge branch 'rebrand-to-nf-schema' into rework-fromSamplesheet
nvnieuwk Mar 20, 2024
4977ec0
convert fromSamplesheet to an operator
nvnieuwk Mar 20, 2024
ba91212
move as much logic as possible to the SamplesheetConverter
nvnieuwk Mar 21, 2024
d28b63c
Make the operator more stable
nvnieuwk Mar 21, 2024
7da6e06
add function equivalent to fromSamplesheet
nvnieuwk Mar 21, 2024
2352139
Merge branch 'rebrand-to-nf-schema' into rework-fromSamplesheet
nvnieuwk Apr 9, 2024
3772bea
update tests
nvnieuwk Apr 9, 2024
9a19944
Merge branch 'rebrand-to-nf-schema' into rework-fromSamplesheet
nvnieuwk Apr 10, 2024
1bfc475
let Nextflow do the file handling
nvnieuwk Apr 11, 2024
25f0b9c
update docs with the changes
nvnieuwk Apr 11, 2024
c84c55e
prettier
nvnieuwk Apr 11, 2024
773e309
fix tests
nvnieuwk Apr 11, 2024
7524e16
Merge branch 'master' into rework-fromSamplesheet
nvnieuwk Apr 11, 2024
5bcd13c
Update CHANGELOG.md
nvnieuwk Apr 15, 2024
cfd0f60
apply review suggestions
nvnieuwk Apr 15, 2024
08d3317
Merge branch 'rework-fromSamplesheet' of github.com:nextflow-io/nf-sc…
nvnieuwk Apr 15, 2024
c971158
fixed error with GString inputs
nvnieuwk Apr 15, 2024
f02b240
Use CharSequence instead of String and GString
nvnieuwk Apr 16, 2024
321c245
add make install as shown in the podcast
nvnieuwk Apr 17, 2024
68117c0
remove fromSamplesheet and only use samplesheetToList
nvnieuwk Apr 18, 2024
131848b
fix tests
nvnieuwk Apr 18, 2024
47514c0
add a small note about the automatic typing in csv or tsv
nvnieuwk Apr 18, 2024
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2 changes: 1 addition & 1 deletion plugins/nf-schema/src/main/nextflow/validation/SchemaValidator.groovy
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Original file line number Diff line number Diff line change
Expand Up @@ -204,7 +204,7 @@ class SchemaValidator extends PluginExtensionPoint {

final target = CH.createBy(source)
final next = {
if(!(it instanceof String || it instanceof Path)) {
if(!(it instanceof String || it instanceof Path || it instanceof GString)) {
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def msg = "${colors.red}The .fromSamplesheet operator only takes a channel with one value per entry (either a String or Path type)\n${colors.reset}\n"
throw new SchemaValidationException(msg)
}
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