Sanitize path

[maxulysse]

Description of the bug

params.outdir + "/path/output/"

->

file(params.outdir + "/path/output/").toUriString()

Command used and terminal output

No response

Relevant files

No response

System information

No response

[adamrtalbot]

For context, the bug is that sometimes the path is resolved to include a double slash. This breaks certain filesystems:

e.g.

params.outdir = '/output/`

params.outdir + /path/ = /output//path/

Using file operations will solve this: https://www.nextflow.io/docs/latest/script.html#opening-files

Options:
file(params.outdir).resolve("path")
file(params.outdir) / "path"
file("${params.outdir}/path") <- path object
file("${params.outdir}/path").toUriString() <- string object

[FriederikeHanssen]

After the recent dicussions, do we still want to fix this here or rather wait for a nextflow fix? This applies to virtually all nf-core pipelines and how they specify the outdir in modules.config

Related issue: #1580

[FriederikeHanssen]

fixed by nextflow as far as I can tell. Any remaining issues are in nf-validation

[allyssonallan]

sarek/conf/test.config

Line 31 in ae4dd11

igenomes_base = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/'

Using test profile:

1. I am getting this error related to the double slash.
   `igenomes_base = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/'``

2. After changing to /data without the end slash, I am getting this error related to the addresses that changed in https://github.com/nf-core/test-datasets/tree/modules/data:

ERROR ~ Validation of pipeline parameters failed!

 -- Check '.nextflow.log' file for details
The following invalid input values have been detected:

* --mappability (https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/Homo_sapiens/GATK/GRCh38/Annotation/Control-FREEC/out100m2_hg38.gem): the file or directory 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/Homo_sapiens/GATK/GRCh38/Annotation/Control-FREEC/out100m2_hg38.gem' does not exist
* --germline_resource_tbi (https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/af-only-gnomad.hg38.vcf.gz.tbi): the file or directory 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/af-only-gnomad.hg38.vcf.gz.tbi' does not exist
* --fasta_fai (https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta.fai): the file or directory 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta.fai' does not exist
* --known_indels (https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels.vcf.gz): the file or directory 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels.vcf.gz' does not exist
* --known_indels_tbi (https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi): the file or directory 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi' does not exist
* --ngscheckmate_bed (https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/Homo_sapiens/GATK/GRCh38/Annotation/NGSCheckMate/SNP_GRCh38_hg38_wChr.bed): the file or directory 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/Homo_sapiens/GATK/GRCh38/Annotation/NGSCheckMate/SNP_GRCh38_hg38_wChr.bed' does not exist
* --fasta (https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta): the file or directory 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta' does not exist
* --known_snps_tbi (https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/1000G_omni2.5.hg38.vcf.gz.tbi): the file or directory 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/1000G_omni2.5.hg38.vcf.gz.tbi' does not exist
* --germline_resource (https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/af-only-gnomad.hg38.vcf.gz): the file or directory 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/af-only-gnomad.hg38.vcf.gz' does not exist
* --known_snps (https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/1000G_omni2.5.hg38.vcf.gz): the file or directory 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/1000G_omni2.5.hg38.vcf.gz' does not exist