check_samplesheet.py script doesn't output optional columns in samplesheet

[adomingues]

Description of the bug

Hi all,

check_samplesheet only saves the required columns* and discards all extra columns, whereas I expecting it to save all columns in the input file. Is my expectation wrong?

*sample,single_end,fastq_1,fastq_2,strandedness

Command used and terminal output

I downloaded the lastest version of the script and then ran it with a modified version of the test samplesheet:

sample	fastq_1	fastq_2	strandedness	treatment	genotype	induction	bio_replicate
WT_REP1	s3://nf-core-awsmegatests/rnaseq/input_data/minimal/GSE110004/SRR6357070_1.fastq.gz	s3://nf-core-awsmegatests/rnaseq/input_data/minimal/GSE110004/SRR6357070_2.fastq.gz	reverse	WT		FALSE	rep1
WT_REP1	s3://nf-core-awsmegatests/rnaseq/input_data/minimal/GSE110004/SRR6357071_1.fastq.gz	s3://nf-core-awsmegatests/rnaseq/input_data/minimal/GSE110004/SRR6357071_2.fastq.gz	reverse	WT		FALSE	rep2
WT_REP2	s3://nf-core-awsmegatests/rnaseq/input_data/minimal/GSE110004/SRR6357072_1.fastq.gz	s3://nf-core-awsmegatests/rnaseq/input_data/minimal/GSE110004/SRR6357072_2.fastq.gz	reverse	WT		FALSE	rep3
RAP1_UNINDUCED_REP1	s3://nf-core-awsmegatests/rnaseq/input_data/minimal/GSE110004/SRR6357073_1.fastq.gz		reverse	RAP1_UNINDUCED		FALSE	rep1
RAP1_UNINDUCED_REP2	s3://nf-core-awsmegatests/rnaseq/input_data/minimal/GSE110004/SRR6357074_1.fastq.gz		reverse	RAP1_UNINDUCED		FALSE	rep2
RAP1_UNINDUCED_REP2	s3://nf-core-awsmegatests/rnaseq/input_data/minimal/GSE110004/SRR6357075_1.fastq.gz		reverse	RAP1_UNINDUCED		FALSE	rep3
RAP1_IAA_30M_REP1	s3://nf-core-awsmegatests/rnaseq/input_data/minimal/GSE110004/SRR6357076_1.fastq.gz	s3://nf-core-awsmegatests/rnaseq/input_data/minimal/GSE110004/SRR6357076_2.fastq.gz	reverse	RAP1_IAA_30M		TRUE	rep1

./check_samplesheet.py 90-785846343.samplesheet.csv valid.samplesheet.csv 

The output contains only the mandatory columns.

sample	single_end	fastq_1	fastq_2	strandedness
RAP1_IAA_30M_REP1_T1	0	s3://nf-core-awsmegatests/rnaseq/input_data/minimal/GSE110004/SRR6357076_1.fastq.gz	s3://nf-core-awsmegatests/rnaseq/input_data/minimal/GSE110004/SRR6357076_2.fastq.gz	reverse
RAP1_UNINDUCED_REP1_T1	1	s3://nf-core-awsmegatests/rnaseq/input_data/minimal/GSE110004/SRR6357073_1.fastq.gz		reverse
RAP1_UNINDUCED_REP2_T1	1	s3://nf-core-awsmegatests/rnaseq/input_data/minimal/GSE110004/SRR6357074_1.fastq.gz		reverse
RAP1_UNINDUCED_REP2_T2	1	s3://nf-core-awsmegatests/rnaseq/input_data/minimal/GSE110004/SRR6357075_1.fastq.gz		reverse
WT_REP1_T1	0	s3://nf-core-awsmegatests/rnaseq/input_data/minimal/GSE110004/SRR6357070_1.fastq.gz	s3://nf-core-awsmegatests/rnaseq/input_data/minimal/GSE110004/SRR6357070_2.fastq.gz	reverse
WT_REP1_T2	0	s3://nf-core-awsmegatests/rnaseq/input_data/minimal/GSE110004/SRR6357071_1.fastq.gz	s3://nf-core-awsmegatests/rnaseq/input_data/minimal/GSE110004/SRR6357071_2.fastq.gz	reverse
WT_REP2_T1	0	s3://nf-core-awsmegatests/rnaseq/input_data/minimal/GSE110004/SRR6357072_1.fastq.gz	s3://nf-core-awsmegatests/rnaseq/input_data/minimal/GSE110004/SRR6357072_2.fastq.gz	reverse

### Relevant files

[samplesheet_test.csv](https://github.com/nf-core/rnaseq/files/10131154/samplesheet_test.csv)
[valid.samplesheet.csv](https://github.com/nf-core/rnaseq/files/10131156/valid.samplesheet.csv)


### System information

local test on an ubuntu machine
Python 3.8.10 & Python 2.7.18 yield the same result

[adomingues]

I somehow messed the bug report, here are the files:

samplesheet_test.csv
valid.samplesheet.csv

[drpatelh]

Fixed in #908

Any additional columns provided in --input will now also be dumped in samplesheet.valid.csv