Harshil Patel

Hi guys! Thanks for posting here and for using the pipeline. I agree that these docs are a little sparse and can be a little confusing. If you are able...

The pipeline should be able to handle additional columns already @grst. Not convinced arbitrary order is a good thing though mainly for standardisation but happy to be persuaded otherwise. Yes,...

Anything fancy we can do here @grst to improve our current implementation? We have now added a stand-alone samplesheet schema to help with the validation in https://github.com/nf-core/rnaseq/pull/623 but there are...

Yeah, I know. That 🐛 is really annoying and I suspect it will be quite an easy fix. Just haven't found a portable way to test it!

Yup, most of the Python stuff would be obsolete! I think the problem is that the validation needs to happen with standard libraries before it is passed to the pipeline...

Testing with this samplesheet: ```console sampe,ft_1,_2,strdedness WT_REP1,https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/testdata/GSE110004/SRR6357070_1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/testdata/GSE110004/SRR6357070_2.fastq.gz,reverse WT_REP2,https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/testdata/GSE110004/SRR6357072_1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/testdata/GSE110004/SRR6357072_2.fastq.gz,reverse ``` I get the following:  Questions: * Doesn't it make sense to only look in the first line for column headers?...

Testing with this samplesheet: ``` sample,fastq_1,fastq_2,strandedness WT_REP1,https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/testdata/GSE110004/SRR6357070_1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/testdata/GSE110004/SRR6357070_2.fastq.gz,reverse WT_REP2,https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/testdata/GSE110004/SRR6357072_1.faq.gz,,reverse ``` I get the following:  Questions: * The offending line is actually `Row 2`. You will notice the file extension is...

Testing with this samplesheet: ``` "sample","fastq_1","fastq_2","strandedness","accession","altitude","assembly_quality","assembly_software","base_count","binning_software","bio_material","broker_name ","cell_line","cell_type","center_name","checklist","collected_by","collection_date","completeness_score","contamination_score","country","cram_index_aspera","cram_i ndex_ftp","cram_index_galaxy","cultivar","culture_collection","depth","description","dev_stage","ecotype","elevation","environment_biome","environment_feature","envi ronment_material","environmental_package","environmental_sample","experiment_accession","experiment_alias","experiment_title","experimental_factor","fastq_aspera","f astq_bytes","fastq_ftp","fastq_galaxy","fastq_md5","first_created","first_public","germline","host","host_body_site","host_genotype","host_gravidity","host_growth_co nditions","host_phenotype","host_sex","host_status","host_tax_id","identified_by","instrument_model","instrument_platform","investigation_type","isolate","isolation_ source","last_updated","lat","library_layout","library_name","library_selection","library_source","library_strategy","location","lon","mating_type","nominal_length", "nominal_sdev","parent_study","ph","project_name","protocol_label","read_count","run_accession","run_alias","salinity","sample_accession","sample_alias","sample_capt ure_status","sample_collection","sample_description","sample_material","sample_title","sampling_campaign","sampling_platform","sampling_site","scientific_name","seco ndary_sample_accession","secondary_study_accession","sequencing_method","serotype","serovar","sex","specimen_voucher","sra_aspera","sra_bytes","sra_ftp","sra_galaxy" ,"sra_md5","strain","study_accession","study_alias","study_title","sub_species","sub_strain","submission_accession","submitted_aspera","submitted_bytes","submitted_f ormat","submitted_ftp","submitted_galaxy","submitted_host_sex","submitted_md5","submitted_sex","target_gene","tax_id" "SRX7777164","./results/public_data/SRX7777164_T1_1.fastq.gz","./results/public_data/SRX7777164_T1_2.fastq.gz","unstranded","SAMN14154203","","","","159508570","","" ,"","","","SUB6993965","","Wisconsin State Lab of Hygiene","2020-02-14","","","USA: Wisconsin, Madison","","","","","","","Illumina MiSeq sequencing; SARS-CoV-2 vero E6_illumina","","","","","","","","false","SRX7777164","veroE6_illumina","Illumina...

The Python script takes the user provided samplesheet as input and re-formats it before it is loaded in NF. This has allowed the validation and tweaking of the samplesheet e.g....

Hmmm....why is it not working for that module in particular when it is for all of the others? Think we need to figure that out. Could you post what the...