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Update fastqingress.nf

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This commit is contained in:
Sarah Griffiths 2023-09-05 08:57:28 +00:00
parent d9ee1034a3
commit 2bda37388c
2 changed files with 8 additions and 8 deletions
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14
lib/fastqingress.nf
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@ -311,7 +311,13 @@ def get_valid_inputs(Map margs){
[create_metamap([alias: margs["sample"] ?: input.baseName]), input]) [create_metamap([alias: margs["sample"] ?: input.baseName]), input])
} else { } else {
// deal with the second case (sub-directories with fastq data) --> first // deal with the second case (sub-directories with fastq data) --> first
// check whether we actually found sub-directories // check whether we actually found sub-directories (and remove
// sub-directories called 'unclassified' unless otherwise specified)
if (!margs.analyse_unclassified) {
sub_dirs_with_fastq_files = sub_dirs_with_fastq_files.findAll {
it.baseName != "unclassified"
}
}
if (!sub_dirs_with_fastq_files) { if (!sub_dirs_with_fastq_files) {
error "Input directory '$input' must contain either FASTQ files " + error "Input directory '$input' must contain either FASTQ files " +
"or sub-directories containing FASTQ files." "or sub-directories containing FASTQ files."
@ -325,12 +331,6 @@ def get_valid_inputs(Map margs){
error "Input directory '$input' cannot contain more " + error "Input directory '$input' cannot contain more " +
"than one level of sub-directories with FASTQ files." "than one level of sub-directories with FASTQ files."
} }
// remove directories called 'unclassified' unless otherwise specified
if (!margs.analyse_unclassified) {
sub_dirs_with_fastq_files = sub_dirs_with_fastq_files.findAll {
it.baseName != "unclassified"
}
}
// filter based on sample sheet in case one was provided // filter based on sample sheet in case one was provided
if (margs.sample_sheet) { if (margs.sample_sheet) {
// get channel of entries in the sample sheet // get channel of entries in the sample sheet

2
nextflow.config
View File

@ -104,7 +104,7 @@ params {
] ]
agent = null agent = null
container_sha = "sha203915eb4b4dd444cb2e845d0b9f7814e26b7b5c" container_sha = "sha203915eb4b4dd444cb2e845d0b9f7814e26b7b5c"
common_sha = "sha5fc720674a26bc63a6f31ed186344209175b54b1" common_sha = "sha0a6dc21fac17291f4acb2e0f67bcdec7bf63e6b7"
} }
} }