Nextflow lint subworkflows fix (nf-core#10123)

Fix index

Author: LouisLeNezet

subworkflows/nf-core/fastq_taxonomic_profile_metaphlan/main.nf

@@ -18,7 +18,7 @@ workflow FASTQ_TAXONOMIC_PROFILE_METAPHLAN {
     ch_versions = ch_versions.mix(METAPHLAN_METAPHLAN.out.versions.first())
 
     metaphlan_merged_profiles_txt = METAPHLAN_MERGEMETAPHLANTABLES(METAPHLAN_METAPHLAN.out.profile
-        .map { meta, profile -> [[id: 'all_samples'], profile] }
+        .map { _meta, profile -> [[id: 'all_samples'], profile] }
         .groupTuple(sort: { profile -> profile.getName() }))
         .txt
     ch_versions = ch_versions.mix(METAPHLAN_MERGEMETAPHLANTABLES.out.versions.first())

subworkflows/nf-core/quantify_rsem/main.nf

@@ -43,8 +43,11 @@ workflow QUANTIFY_RSEM {
     // Merge counts across samples
     //
     CUSTOM_RSEMMERGECOUNTS (
-        ch_counts_gene.collect{ index -> index[1] }.map { results -> [ ['id': 'all_samples'], results ] },
-        ch_counts_transcript.collect{ index -> index[1] }
+        ch_counts_gene
+            .collect{ _meta, genes_count -> genes_count }
+            .map { genes_count -> [ ['id': 'all_samples'], genes_count ] },
+        ch_counts_transcript
+            .collect{ _meta, transcripts_count -> transcripts_count }
     )
 
     //