Nextflow deepTools fingerprint - nextflow

Question

I am trying to use nextflow pipeline to do a fringerprint(bamCoverage) from deeptool. When I input the bam files and run the script. it says I don't have index files. error: [E::idx_find_and_load] Could not retrieve index file for 'Kasumi_NCOR1.genome.sorted.bam'
[E::idx_find_and_load] Could not retrieve index file for 'Kasumi_NCOR1.genome.sorted.bam'
'Kasumi_NCOR1.genome.sorted.bam' does not appear to have an index. You MUST index the file first!
process fingerprint_cov {
publishDir "${params.outdir}/fingerprint_cov", mode: 'copy'
input:
set val(sample_id), file(samples) from sorted_bam_sample_control_ch.samples
set val(sample_id_c), file(controls) from sorted_bam_sample_control_ch.controls
output:
set val(sample_id), file("${sample_id}.cov.bedgraph") into sample_cov_ch
set val(sample_id_c), file("${sample_id_c}.cov.bedgraph") into control_cov_ch
script:
"""
bamCoverage -b ${samples} -o ${sample_id}.cov.bedgraph -of bedgraph -bs 1000 -p 10
bamCoverage -b ${controls} -o ${sample_id_c}.cov.bedgraph -of bedgraph -bs 1000 -p 10
"""
}
sorted_bam_sample_control_ch.samples has all the sample bam files, and sorted_bam_sample_control_ch.control has the control bam files. How do I input the bam.bai files? I have also seen that output bam and bam.bai to a channel, but how to process this steps?
This is my sample input. but when I run the process it only runs one sample
[Kasumi_H3K36, [/mnt/Data/cut_and_tag/work/0c/24e138a92a1eb0d906e1e9fad9ba4b/Kasumi_H3K36.genome.sorted.bam, /mnt/Data/cut_and_tag/work/0c/24e138a92a1eb0d906e1e9fad9ba4b/Kasumi_H3K36.genome.sorted.bam.bai]]
[Kasumi_H4K5, [/mnt/Data/cut_and_tag/work/7e/a740e11ce39f2a310b749603c785a4/Kasumi_H4K5.genome.sorted.bam, /mnt/Data/cut_and_tag/work/7e/a740e11ce39f2a310b749603c785a4/Kasumi_H4K5.genome.sorted.bam.bai]]
[Kasumi_NCOR1, [/mnt/Data/cut_and_tag/work/b8/e91ff7c7aea0fa3a0814530ab07972/Kasumi_NCOR1.genome.sorted.bam, /mnt/Data/cut_and_tag/work/b8/e91ff7c7aea0fa3a0814530ab07972/Kasumi_NCOR1.genome.sorted.bam.bai]]
[Kasumi_JMJD1C, [/mnt/Data/cut_and_tag/work/49/99ebe402d2b1953a95968525e258f6/Kasumi_JMJD1C.genome.sorted.bam, /mnt/Data/cut_and_tag/work/49/99ebe402d2b1953a95968525e258f6/Kasumi_JMJD1C.genome.sorted.bam.bai]]
Here is the control input
[Kasumi_IgG, [/mnt/Data/cut_and_tag/work/0e/1cd7aefd90105205e58fb6ef912aa4/Kasumi_IgG.genome.sorted.bam, /mnt/Data/cut_and_tag/work/0e/1cd7aefd90105205e58fb6ef912aa4/Kasumi_IgG.genome.sorted.bam.bai]]

Answer 1

You'll need to index your BAM files first if the index (.bai) files don't already exist. You can use samtools index <bam> for this.
Then all you would need to do is input these into your process somehow. Rather than having a separate variable in each of your input sets/tuples, what I find works quite nicely is grouping the BAM files and their indexes in a tuple of the form: tuple( bam, bai )
Then your process might look like:
process fingerprint_cov {
publishDir "${params.outdir}/fingerprint_cov", mode: 'copy'
input:
set val(test_sample_id), file(indexed_test_bam) from sorted_bam_sample_control_ch.samples
set val(control_sample_id), file(indexed_control_bam) from sorted_bam_sample_control_ch.controls
output:
set val(test_sample_id), file("${test_sample_id}.cov.bedgraph") into sample_cov_ch
set val(control_sample_id), file("${control_sample_id}.cov.bedgraph") into control_cov_ch
script:
def test_bam = indexed_test_bam.first()
def control_bam = indexed_control_bam.first()
"""
bamCoverage -b "${test_bam}" -o "${sample_id}.cov.bedgraph" -of bedgraph -bs 1000 -p 10
bamCoverage -b "${control_bam}" -o "${sample_id_c}.cov.bedgraph" -of bedgraph -bs 1000 -p 10
"""
}