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Fix linting from a comment

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fix_linting.yml
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Add fq2bam to methylseq Fix linting from a comment #98: Issue comment #592 (comment) created by nf-core-bot
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Filter Bismark coverage files in targeted sequencing mode Fix linting from a comment #97: Issue comment #604 (comment) created by nf-core-bot
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DOCS: remove --genome GRCh38 from docs for testing the pipeline Fix linting from a comment #96: Issue comment #603 (comment) created by nf-core-bot
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DOCS: remove --genome GRCh38 from docs for testing the pipeline Fix linting from a comment #95: Issue comment #602 (comment) created by nf-core-bot
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refactor: migrate to nf-core-utils plugin Fix linting from a comment #94: Issue comment #598 (comment) created by nf-core-bot
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Preview: Record types Fix linting from a comment #93: Issue comment #593 (comment) created by bentsherman
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Preview: Record types Fix linting from a comment #92: Issue comment #593 (comment) created by bentsherman
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Preview: Record types Fix linting from a comment #91: Issue comment #593 (comment) created by ewels
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Preview: Record types Fix linting from a comment #90: Issue comment #593 (comment) created by bentsherman
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Preview: Record types Fix linting from a comment #89: Issue comment #593 (comment) created by ewels
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Preview: Record types Fix linting from a comment #88: Issue comment #593 (comment) created by bentsherman
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Preview: Record types Fix linting from a comment #87: Issue comment #593 (comment) created by nf-core-bot
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Support analysis of spike-in sequences Fix linting from a comment #86: Issue comment #97 (comment) created by katestan
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—skip_deduplication flag does not activate duplication skipping Fix linting from a comment #85: Issue comment #575 (comment) created by kmkappa
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Add fq2bam to methylseq Fix linting from a comment #84: Issue comment #592 (comment) created by eduard-watchmaker
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Add fq2bam to methylseq Fix linting from a comment #83: Issue comment #592 (comment) created by eduard-watchmaker
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Add fq2bam to methylseq Fix linting from a comment #82: Issue comment #592 (comment) created by eduard-watchmaker
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Add fq2bam to methylseq Fix linting from a comment #81: Issue comment #592 (comment) created by eduard-watchmaker
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Running in -stub mode fails for BISMARK_SUMMARY Fix linting from a comment #80: Issue comment #527 (comment) created by sateeshperi
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—skip_deduplication flag does not activate duplication skipping Fix linting from a comment #79: Issue comment #575 (comment) created by sateeshperi
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--rrbs samtools sort bam incorrectly named with deduplicated prefix Fix linting from a comment #78: Issue comment #579 (comment) created by sateeshperi
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--aligner bwameth samtools sort bam incorrectly named with deduplicated prefix Fix linting from a comment #77: Issue comment #580 (comment) created by sateeshperi
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Workflow exits after TrimGalore with “successful” status but no alignments produced Fix linting from a comment #76: Issue comment #589 (comment) created by sateeshperi
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Workflow exits after TrimGalore with “successful” status but no alignments produced Fix linting from a comment #75: Issue comment #589 (comment) created by sansense
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Workflow exits after TrimGalore with “successful” status but no alignments produced Fix linting from a comment #74: Issue comment #589 (comment) created by sansense
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