Description of the bug
The samplesheet used by the test_full profile is still using old S3 paths for test input data. These should be corrected to the new S3 paths.
I've edited the samplesheet content (at https://ngi-igenomes.s3.amazonaws.com/test-data/mag/samplesheets/samplesheet.full.csv) to contain corrected new S3 paths that work at present:
sample,group,short_reads_1,short_reads_2,long_reads
CAPES_S11,0,s3://ngi-igenomes/test-data/mag/ERR3201918_1.fastq.gz,s3://ngi-igenomes/test-data/mag/ERR3201918_2.fastq.gz,s3://ngi-igenomes/test-data/mag/ERR3201942.fastq.gz
CAPES_S21,0,s3://ngi-igenomes/test-data/mag/ERR3201928_1.fastq.gz,s3://ngi-igenomes/test-data/mag/ERR3201928_2.fastq.gz,s3://ngi-igenomes/test-data/mag/ERR3201952.fastq.gz
CAPES_S7,0,s3://ngi-igenomes/test-data/mag/ERR3201914_1.fastq.gz,s3://ngi-igenomes/test-data/mag/ERR3201914_2.fastq.gz,s3://ngi-igenomes/test-data/mag/ERR3201938.fastq.gz
The paths for other input files specified in the master test_full.config are corrected in the dev branch test_full.config.
Command used and terminal output
Running with the test_full profile:
nextflow run nf-core/mag -r dev -profile test_full,singularity --outdir test_full_output
Returns the following error:
No such file: s3://nf-core-awsmegatests/mag/input_data/ERR3201918_1.fastq.gz
Relevant files
No response
System information
No response
Description of the bug
The samplesheet used by the
test_fullprofile is still using old S3 paths for test input data. These should be corrected to the new S3 paths.I've edited the samplesheet content (at https://ngi-igenomes.s3.amazonaws.com/test-data/mag/samplesheets/samplesheet.full.csv) to contain corrected new S3 paths that work at present:
The paths for other input files specified in the master test_full.config are corrected in the dev branch test_full.config.
Command used and terminal output
Running with the test_full profile:
Returns the following error:
Relevant files
No response
System information
No response