Some polyGs at the end of the sequences are not removed

Hi Marcel,

I'm using cutadapt v5.1 and python v3.12.11 and I used pip for the installation.

This is the code I have in my pipeline:
cutadapt -m {config[minlength]} --nextseq-trim={params.nextseqTrim} --max-n {config[maxn]} -a {config[fwd_adapter]} -A {config[rev_adapter]} -j {config[metqc_cpus]} -o {output.r1} -p {output.r2}
{input.r1} {input.r2}

`Raw input forward read example:
@VL00845:28:222HWCNNX:1:1415:77502:26573 1:N:0:AACCGTTGCT+GACTCTTACT
GTTTTATAAGAGTCTTGGATTTGAAGTAATTATGCAGTCTTATAATGAAAAAGCAGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGC
+
IIIIIIIIIIIIII9IIIIIIIIIIIIIIII9IIIIIIIII9IIIIIIIIIIIIIIIIIII99IIIII9II99I99IIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9II99I9IIIIII9IIIIIII99IIIII9
@VL00845:28:222HWCNNX:1:1415:77982:26573 1:N:0:AACCGTTGCT+GACTCTTACT

`

`Cutadapt produced forward read example:

@VL00845:28:222HWCNNX:1:1415:77502:26573 1:N:0:AACCGTTGCT+GACTCTTACT
GTTTTATAAGAGTCTTGGATTTGAAGTAATTATGCAGTCTTATAATGAAAAAGCAGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGC
+
IIIIIIIIIIIIII9IIIIIIIIIIIIIIII9IIIIIIIII9IIIIIIIIIIIIIIIIIII99IIIII9II99I99IIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9II99I9IIIIII9IIIIIII99IIIII9
@VL00845:28:222HWCNNX:1:1415:77982:26573 1:N:0:AACCGTTGCT+GACTCTTACT

`

`Expected Cutadapt produced forward read example:

@VL00845:28:222HWCNNX:1:1415:77502:26573 1:N:0:AACCGTTGCT+GACTCTTACT
GTTTTATAAGAGTCTTGGATTTGAAGTAATTATGCAGTCTTATAATGAAAAAGCA
`

By checking more reads, it seems like cutadapt doesn't remove polyGs when they appear in the beginning and in the middle (stated in the documentation as well) or when there are some ATCG nucleotides present after polyGs at the end of the sequences. I was wondering if this is expected and what would be the best way of dealing with these polyG sequences that mess up the GC content figures of the quality control tools.

I was also wondering if it's ok to do adapter and quality trimming in one command since adapter trimming is done after quality trimming and before length trimming. Does this affect adapter trimming alone or quality trimming alone? Should I separate them and do them in two steps?

Thanks

Reproduce the reported behavior with cutadapt v5.1 using the provided paired-read command, especially --nextseq-trim and the -a/-A adapter options. Read the trimming-order documentation and inspect the handling of terminal, internal, and interrupted poly-G runs; done means determining whether the output is expected and identifying the required documentation or behavior change.