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Pipeline updates / addressing open issues #770

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merged 9 commits into from
Feb 21, 2022
Merged

Pipeline updates / addressing open issues #770

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df102cd
Add --publish_dir_mode back into pipeline #752
drpatelh Feb 20, 2022
71c0d38
Fix #759
drpatelh Feb 20, 2022
d55892b
Fix #744
drpatelh Feb 20, 2022
24c69fb
Update CHANGELOG
drpatelh Feb 20, 2022
6775dc3
Fix ECLint
drpatelh Feb 20, 2022
091f952
Fix process selector for CUSTOM_GETCHROMSIZES
drpatelh Feb 20, 2022
a7915a6
Fix #753
drpatelh Feb 20, 2022
f1146a2
Fix ECLint
drpatelh Feb 20, 2022
47814c9
Easy fix for #754
drpatelh Feb 20, 2022
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18 changes: 18 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -7,8 +7,26 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### Enhancements & fixes

* [[#734](https://github.com/nf-core/rnaseq/issues/734)] - Is a vulnerable picard still used ? log4j vulnerability
* [[#744](https://github.com/nf-core/rnaseq/issues/744)] - Auto-detect and raise error if CSI is required for BAM indexing
* [[#752](https://github.com/nf-core/rnaseq/issues/752)] - How to set publishing mode for all processes?
* [[#753](https://github.com/nf-core/rnaseq/issues/753)] - Add warning when user provides `--transcript_fasta`
* [[#754](https://github.com/nf-core/rnaseq/issues/754)] - DESeq2 QC issue linked to `--count_col` parameter
* [[#755](https://github.com/nf-core/rnaseq/issues/755)] - Rename RSEM_PREPAREREFERENCE_TRANSCRIPTS process
* [[#759](https://github.com/nf-core/rnaseq/issues/759)] - Empty lines in samplesheet.csv cause a crash

### Parameters

| Old parameter | New parameter |
|-------------------------------|---------------------------------------|
| | `--publish_dir_mode` |

> **NB:** Parameter has been **updated** if both old and new parameter information is present.
>
> **NB:** Parameter has been **added** if just the new parameter information is present.
>
> **NB:** Parameter has been **removed** if new parameter information isn't present.

## [[3.5](https://github.com/nf-core/rnaseq/releases/tag/3.5)] - 2021-12-17

### Enhancements & fixes
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129 changes: 65 additions & 64 deletions bin/check_samplesheet.py
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Expand Up @@ -61,79 +61,80 @@ def check_samplesheet(file_in, file_out):

## Check sample entries
for line in fin:
lspl = [x.strip().strip('"') for x in line.strip().split(",")]

## Check valid number of columns per row
if len(lspl) < len(HEADER):
print_error(
f"Invalid number of columns (minimum = {len(HEADER)})!",
"Line",
line,
)

num_cols = len([x for x in lspl if x])
if num_cols < MIN_COLS:
print_error(
f"Invalid number of populated columns (minimum = {MIN_COLS})!",
"Line",
line,
)

## Check sample name entries
sample, fastq_1, fastq_2, strandedness = lspl[: len(HEADER)]
if sample.find(" ") != -1:
print(
f"WARNING: Spaces have been replaced by underscores for sample: {sample}"
)
sample = sample.replace(" ", "_")
if not sample:
print_error("Sample entry has not been specified!", "Line", line)

## Check FastQ file extension
for fastq in [fastq_1, fastq_2]:
if fastq:
if fastq.find(" ") != -1:
print_error("FastQ file contains spaces!", "Line", line)
if not fastq.endswith(".fastq.gz") and not fastq.endswith(".fq.gz"):
if line.strip():
lspl = [x.strip().strip('"') for x in line.strip().split(",")]

## Check valid number of columns per row
if len(lspl) < len(HEADER):
print_error(
f"Invalid number of columns (minimum = {len(HEADER)})!",
"Line",
line,
)

num_cols = len([x for x in lspl if x])
if num_cols < MIN_COLS:
print_error(
f"Invalid number of populated columns (minimum = {MIN_COLS})!",
"Line",
line,
)

## Check sample name entries
sample, fastq_1, fastq_2, strandedness = lspl[: len(HEADER)]
if sample.find(" ") != -1:
print(
f"WARNING: Spaces have been replaced by underscores for sample: {sample}"
)
sample = sample.replace(" ", "_")
if not sample:
print_error("Sample entry has not been specified!", "Line", line)

## Check FastQ file extension
for fastq in [fastq_1, fastq_2]:
if fastq:
if fastq.find(" ") != -1:
print_error("FastQ file contains spaces!", "Line", line)
if not fastq.endswith(".fastq.gz") and not fastq.endswith(".fq.gz"):
print_error(
"FastQ file does not have extension '.fastq.gz' or '.fq.gz'!",
"Line",
line,
)

## Check strandedness
strandednesses = ["unstranded", "forward", "reverse"]
if strandedness:
if strandedness not in strandednesses:
print_error(
"FastQ file does not have extension '.fastq.gz' or '.fq.gz'!",
f"Strandedness must be one of '{', '.join(strandednesses)}'!",
"Line",
line,
)

## Check strandedness
strandednesses = ["unstranded", "forward", "reverse"]
if strandedness:
if strandedness not in strandednesses:
else:
print_error(
f"Strandedness must be one of '{', '.join(strandednesses)}'!",
f"Strandedness has not been specified! Must be one of {', '.join(strandednesses)}.",
"Line",
line,
)
else:
print_error(
f"Strandedness has not been specified! Must be one of {', '.join(strandednesses)}.",
"Line",
line,
)

## Auto-detect paired-end/single-end
sample_info = [] ## [single_end, fastq_1, fastq_2, strandedness]
if sample and fastq_1 and fastq_2: ## Paired-end short reads
sample_info = ["0", fastq_1, fastq_2, strandedness]
elif sample and fastq_1 and not fastq_2: ## Single-end short reads
sample_info = ["1", fastq_1, fastq_2, strandedness]
else:
print_error("Invalid combination of columns provided!", "Line", line)

## Create sample mapping dictionary = {sample: [[ single_end, fastq_1, fastq_2, strandedness ]]}
if sample not in sample_mapping_dict:
sample_mapping_dict[sample] = [sample_info]
else:
if sample_info in sample_mapping_dict[sample]:
print_error("Samplesheet contains duplicate rows!", "Line", line)

## Auto-detect paired-end/single-end
sample_info = [] ## [single_end, fastq_1, fastq_2, strandedness]
if sample and fastq_1 and fastq_2: ## Paired-end short reads
sample_info = ["0", fastq_1, fastq_2, strandedness]
elif sample and fastq_1 and not fastq_2: ## Single-end short reads
sample_info = ["1", fastq_1, fastq_2, strandedness]
else:
print_error("Invalid combination of columns provided!", "Line", line)

## Create sample mapping dictionary = {sample: [[ single_end, fastq_1, fastq_2, strandedness ]]}
if sample not in sample_mapping_dict:
sample_mapping_dict[sample] = [sample_info]
else:
sample_mapping_dict[sample].append(sample_info)
if sample_info in sample_mapping_dict[sample]:
print_error("Samplesheet contains duplicate rows!", "Line", line)
else:
sample_mapping_dict[sample].append(sample_info)

## Write validated samplesheet with appropriate columns
if len(sample_mapping_dict) > 0:
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2 changes: 1 addition & 1 deletion bin/deseq2_qc.r
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Expand Up @@ -30,7 +30,7 @@ library(pheatmap)

option_list <- list(
make_option(c("-i", "--count_file" ), type="character", default=NULL , metavar="path" , help="Count file matrix where rows are genes and columns are samples." ),
make_option(c("-f", "--count_col" ), type="integer" , default=2 , metavar="integer", help="First column containing sample count data." ),
make_option(c("-f", "--count_col" ), type="integer" , default=3 , metavar="integer", help="First column containing sample count data." ),
make_option(c("-d", "--id_col" ), type="integer" , default=1 , metavar="integer", help="Column containing identifiers to be used." ),
make_option(c("-r", "--sample_suffix" ), type="character", default='' , metavar="string" , help="Suffix to remove after sample name in columns e.g. '.rmDup.bam' if 'DRUG_R1.rmDup.bam'."),
make_option(c("-o", "--outdir" ), type="character", default='./' , metavar="path" , help="Output directory." ),
Expand Down
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