diff --git a/CHANGELOG.md b/CHANGELOG.md
index 12e1fedd0..db8350977 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -22,7 +22,8 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 * [#302](https://github.com/nf-core/eager/issues/302) - Added mitochondrial to nuclear ratio calculation
 * [#302](https://github.com/nf-core/eager/issues/302) - Added VCF2Genome for concensus sequence generation
 * Fancy new logo from [ZandraFagernas](https://github.com/ZandraFagernas)
-* [#286](https://github.com/nf-core/eager/issues/286) Adds pipeline-specific profiles (loaded from nf-core configs)
+* [#286](https://github.com/nf-core/eager/issues/286) - Adds pipeline-specific profiles (loaded from nf-core configs)
+* [#310](https://github.com/nf-core/eager/issues/310) - Generalises base.config
 
 ### `Fixed`
 
diff --git a/conf/base.config b/conf/base.config
index 04606b41f..e8d193a08 100644
--- a/conf/base.config
+++ b/conf/base.config
@@ -11,79 +11,85 @@
 
 process {
   cpus = { check_max( 1 * task.attempt, 'cpus' ) }
-  memory = { check_max( 8.GB * task.attempt, 'memory' ) }
+  memory = { check_max( 4.GB * task.attempt, 'memory' ) }
   time = { check_max( 2.h * task.attempt, 'time' ) }
 
   errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'finish' }
-  maxRetries = 1
+  maxRetries = 3
   maxErrors = '-1'
 
-  // Process-specific resource requirements (others leave at default, e.g. Fastqc)
-  withName:get_software_versions {
-    memory = { check_max( 2.GB, 'memory' ) }
-    cache = false
+  // Generic resource requirements - s(ingle)c(ore)/m(ulti)c(ore)
+
+  withLabel:'sc_tiny'{
+      cpus = { check_max( 1, 'cpus' ) }
+      memory = { check_max( 1.GB * task.attempt, 'memory' ) }
+      time = { check_max( 2.h * task.attempt, 'time' ) }
   }
-  withName:convertBam {
-    cpus = { check_max(8 * task.attempt, 'cpus') }
+
+  withLabel:'sc_small'{
+      cpus = { check_max( 1, 'cpus' ) }
+      memory = { check_max( 4.GB * task.attempt, 'memory' ) }
+      time = { check_max( 2.h * task.attempt, 'time' ) }
   }
-  withName:makeSeqDict {
-    memory = { check_max( 16.GB * task.attempt, 'memory' ) }
+
+  withLabel:'sc_medium'{
+      cpus = { check_max( 1, 'cpus' ) }
+      memory = { check_max( 8.GB * task.attempt, 'memory' ) }
+      time = { check_max( 2.h * task.attempt, 'time' ) }
   }
-  withname:makeBWAIndex {
-    time = params.large_ref ? '12.h' : { check_max(8.h * task.attempt, 'time') }
+
+  withLabel:'mc_small'{
+      cpus = { check_max( 2, 'cpus' ) }
+      memory = { check_max( 4.GB * task.attempt, 'memory' ) }
+      time = { check_max( 2.h * task.attempt, 'time' ) }
   }
-  withName:bwa {
-    memory = { check_max( 16.GB * task.attempt, 'memory' ) }
-    cpus = { check_max(8 * task.attempt, 'cpus') }
-    time = { check_max(8.h * task.attempt, 'time') }
+
+  withLabel:'mc_medium' {
+      cpus = { check_max( 4, 'cpus' ) }
+      memory = { check_max( 8.GB * task.attempt, 'memory' ) }
+      time = { check_max( 2.h * task.attempt, 'time' ) }
   }
-  withName:bwamem{
-    memory = { check_max( 16.GB * task.attempt, 'memory' ) }
-    cpus = { check_max(8 * task.attempt, 'cpus') }
-    time = { check_max(8.h * task.attempt, 'time') }
+
+  withLabel:'mc_large'{
+      cpus = { check_max( 8, 'cpus' ) }
+      memory = { check_max( 16.GB * task.attempt, 'memory' ) }
+      time = { check_max( 2.h * task.attempt, 'time' ) }
   }
-  withName:qualimap{
-    cpus = { check_max(8 * task.attempt, 'cpus') }
-    errorStrategy = 'ignore'
+
+  withLabel:'mc_huge'{
+      cpus = { check_max( 32, 'cpus' ) }
+      memory = { check_max( 256.GB * task.attempt, 'memory' ) }
+      time = { check_max( 2.h * task.attempt, 'time' ) }
   }
-  withName:bam_trim{
-    cpus = { check_max(4 * task.attempt, 'cpus') }
+
+  // Process-specific resource requirements (others leave at default, e.g. Fastqc)
+  withName:get_software_versions {
+    memory = { check_max( 2.GB, 'memory' ) }
+    cache = false
+  }
+
+  withName:strip_input_fastq {
+     time = { check_max( 4.h * task.attempt, 'time' ) }
   }
-  withName:markDup{
-    cpus = { check_max(8 * task.attempt, 'cpus') }
+
+  withName:qualimap{
+    errorStrategy = 'ignore'
   }
+
   withName:preseq {
     errorStrategy = 'ignore'
   }
-  withName: fastqc {
-    errorStrategy = { task.exitStatus in [143,137] ? 'retry' : 'ignore' }
+
+  // Add 141 ignore due to unclean pipe closing by pmdtools https://github.com/pontussk/PMDtools/issues/7
+  withName: pmdtools {
+    errorStrategy = { task.exitStatus in [141] ? 'ignore' : 'retry' }
   }
+
   withName: multiqc {
     errorStrategy = { task.exitStatus in [143,137] ? 'retry' : 'ignore' }
   }
-  withName: damageprofiler {
-    time = params.large_ref ? { check_max(8.h * task.attempt, 'time') } : { check_max(2.h * task.attempt, 'time')}
-  }
-  withName: strip_input_fastq {
-    cpus = { check_max(8 * task.attempt, 'cpus') }
-    memory = { check_max( 8.GB * task.attempt, 'memory' ) }
-  }
-  withName: malt {
-    memory = { check_max( 128.GB * task.attempt, 'memory' ) }
-    cpus = { check_max(16 * task.attempt, 'cpus') }
-    time = { check_max(2.h * task.attempt, 'time') }
-  }
-  withName: maltextract {
-    memory = { check_max( 8.GB * task.attempt, 'memory' ) }
-    cpus = { check_max(4 * task.attempt, 'cpus') }
-  }
-  withName: vcf2genome {
-    memory = { check_max( 4.GB * task.attempt, 'memory' ) }
-    cpus =  1
-  }
 }
 
-
 params {
   // Defaults only, expecting to be overwritten
   max_memory = 128.GB
diff --git a/docs/usage.md b/docs/usage.md
index feec1a536..a624da2cb 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -114,7 +114,7 @@ Use this parameter to choose a configuration profile. Profiles can give configur
 For more details on how to set up your own private profile, please see [installation](../configuration/adding_your_own.md).
 
 **Basic profiles**
-These are basic profiles which primarily define where you derive the pipeline's software packages from. These are typically the profiles you would use if you are running the pipeline on your **own PC*- (vs. a HPC cluster - see below).
+These are basic profiles which primarily define where you derive the pipeline's software packages from. These are typically the profiles you would use if you are running the pipeline on your **own PC** (vs. a HPC cluster - see below).
 
 - `awsbatch`
   - A generic configuration profile to be used with AWS Batch.
@@ -274,7 +274,7 @@ The output directory where the results will be saved.
 
 #### `-w / -work-dir`
 
-The output directory where _intermediate_ files will be saved. It is **highly recommended*- that this is the same path as `--outdir`, otherwise you may 'lose' your intermediate files if you need to re-run a pipeline. By default, if this flag is not given, the intermediate files will be saved in a `work/` and `.nextflow/` directory from wherever you have run EAGER from.
+The output directory where _intermediate_ files will be saved. It is **highly recommended** that this is the same path as `--outdir`, otherwise you may 'lose' your intermediate files if you need to re-run a pipeline. By default, if this flag is not given, the intermediate files will be saved in a `work/` and `.nextflow/` directory from wherever you have run EAGER from.
 
 ### Optional Reference Options
 
diff --git a/environment.yml b/environment.yml
index a1eb6c206..4b18f99d6 100644
--- a/environment.yml
+++ b/environment.yml
@@ -12,7 +12,7 @@ dependencies:
   - bioconda::picard=2.21.4
   - bioconda::samtools=1.9
   - bioconda::dedup=0.12.5
-  - bioconda::angsd=0.931
+  - bioconda::angsd=0.921
   - bioconda::circularmapper=1.93.4
   - bioconda::gatk4=4.1.4.1
   - bioconda::qualimap=2.2.2d
diff --git a/main.nf b/main.nf
index a1b8324b7..7c107f5bf 100644
--- a/main.nf
+++ b/main.nf
@@ -252,7 +252,7 @@ if ( params.fasta.isEmpty () ){
         file zipped_fasta
 
         output:
-        file "*.{fa,fn,fna,fasta}" into fasta_for_indexing
+        file "*.{fa,fn,fna,fasta}" into ch_fasta_for_bwaindex,ch_fasta_for_faidx,ch_fasta_for_seqdict,ch_fasta_for_circulargenerator,ch_fasta_for_circularmapper,ch_fasta_for_damageprofiler,ch_fasta_for_qualimap,ch_fasta_for_pmdtools,ch_fasta_for_genotyping_ug,ch_fasta_for_genotyping_hc,ch_fasta_for_genotyping_freebayes,ch_fasta_for_vcf2genome,ch_fasta_for_multivcfanalyzer
 
         script:
         rm_zip = zipped_fasta - '.gz'
@@ -262,7 +262,10 @@ if ( params.fasta.isEmpty () ){
         }
        
     } else {
-    fasta_for_indexing = file("${params.fasta}")
+    fasta_for_indexing = Channel
+    .fromPath("${params.fasta}", checkIfExists: true)
+    .into{ ch_fasta_for_bwaindex; ch_fasta_for_faidx; ch_fasta_for_seqdict; ch_fasta_for_circulargenerator; ch_fasta_for_circularmapper; ch_fasta_for_damageprofiler; ch_fasta_for_qualimap; ch_fasta_for_pmdtools; ch_fasta_for_genotyping_ug; ch_fasta__for_genotyping_hc; ch_fasta_for_genotyping_hc; ch_fasta_for_genotyping_freebayes; ch_fasta_for_vcf2genome; ch_fasta_for_multivcfanalyzer }
+    
     lastPath = params.fasta.lastIndexOf(File.separator)
     bwa_base = params.fasta.substring(lastPath+1)
 }
@@ -648,6 +651,7 @@ ${summary.collect { k,v -> "            <dt>$k</dt><dd><samp>${v ?: '<span style
 
 if(!params.bwa_index && !params.fasta.isEmpty() && (params.mapper == 'bwaaln' || params.mapper == 'bwamem' || params.mapper == 'circularmapper')){
 process makeBWAIndex {
+    label 'sc_medium'
     tag {fasta}
     publishDir path: "${params.outdir}/reference_genome/bwa_index", mode: 'copy', saveAs: { filename -> 
             if (params.saveReference) filename 
@@ -656,7 +660,7 @@ process makeBWAIndex {
     }
 
     input:
-    file fasta from fasta_for_indexing
+    file fasta from ch_fasta_for_bwaindex
     file where_are_my_files
 
     output:
@@ -687,6 +691,7 @@ if (params.fasta_index != '') {
 }
 
 process makeFastaIndex {
+    label 'sc_small'
     tag {fasta}
     publishDir path: "${params.outdir}/reference_genome/fasta_index", mode: 'copy', saveAs: { filename -> 
             if (params.saveReference) filename 
@@ -697,7 +702,7 @@ process makeFastaIndex {
     when: params.fasta_index == '' && !params.fasta.isEmpty() && ( params.mapper == 'bwaaln' || params.mapper == 'bwamem' || params.mapper == 'circularmapper')
 
     input:
-    file fasta from fasta_for_indexing
+    file fasta from ch_fasta_for_faidx
     file where_are_my_files
 
     output:
@@ -732,6 +737,7 @@ if (params.seq_dict != '') {
 
 
 process makeSeqDict {
+    label 'sc_medium'
     tag {fasta}
     publishDir path: "${params.outdir}/reference_genome/seq_dict", mode: 'copy', saveAs: { filename -> 
             if (params.saveReference) filename 
@@ -742,7 +748,7 @@ process makeSeqDict {
     when: params.seq_dict == '' && !params.fasta.isEmpty()
 
     input:
-    file fasta from fasta_for_indexing
+    file fasta from ch_fasta_for_seqdict
     file where_are_my_files
 
     output:
@@ -763,6 +769,7 @@ ch_dict_for_skipdict.mix(ch_seq_dict)
 */ 
 
 process convertBam {
+    label 'mc_small'
     tag "$bam"
     
     when: 
@@ -782,10 +789,13 @@ process convertBam {
 }
 
 /*
-* PREPROCESSING - Index a input BAM if not being converted to FASTAPQ
+* PREPROCESSING - Index a input BAM if not being converted to FASTQ
 */
 
 process indexinputbam {
+  label 'sc_small'
+  tag "$prefix"
+
   when: 
   params.bam && !params.run_convertbam
 
@@ -796,12 +806,11 @@ process indexinputbam {
   file "*.{bai,csi}" into ch_mappingindex_for_skipmapping,ch_filteringindex_for_skiprmdup
 
   script:
-    size = "${params.large_ref}" ? '-c' : ''
-    prefix = "${bam.baseName}"
+  size = "${params.large_ref}" ? '-c' : ''
+  prefix = "${bam.baseName}"
   """
-    samtools index "${size}" ${bam}
+  samtools index "${size}" ${bam}
   """
-
 }
 
 // convertbam bypass
@@ -814,12 +823,11 @@ if (params.run_convertbam) {
       .into { ch_convertbam_for_fastp; ch_convertbam_for_skipfastp; ch_convertbam_for_fastqc; ch_convertbam_for_stripfastq } 
 }
 
-
-
 /*
  * STEP 1a - FastQC
  */
 process fastqc {
+    label 'sc_tiny'
     tag "$name"
     publishDir "${params.outdir}/FastQC/input_fastq", mode: 'copy',
         saveAs: {filename -> filename.indexOf(".zip") > 0 ? "zips/$filename" : "$filename"}
@@ -848,6 +856,7 @@ process fastqc {
 */
 
 process fastp {
+    label 'mc_small'
     tag "$name"
     publishDir "${params.outdir}/FastP", mode: 'copy'
 
@@ -890,6 +899,7 @@ if (params.complexity_filter_poly_g) {
  */
 
 process adapter_removal {
+    label 'mc_small'
     tag "$name"
     publishDir "${params.outdir}/read_merging", mode: 'copy'
 
@@ -979,6 +989,7 @@ if (!params.skip_adapterremoval) {
 * STEP 2b - FastQC after clipping/merging (if applied!)
 */
 process fastqc_after_clipping {
+    label 'sc_tiny'
     tag "${name}"
     publishDir "${params.outdir}/FastQC/after_clipping", mode: 'copy',
         saveAs: {filename -> filename.indexOf(".zip") > 0 ? "zips/$filename" : "$filename"}
@@ -1003,6 +1014,7 @@ Step 3a  - Mapping with BWA, SAM to BAM, Sort BAM
 */
 
 process bwa {
+    label 'mc_medium'
     tag "${name}"
     publishDir "${params.outdir}/mapping/bwa", mode: 'copy'
 
@@ -1043,6 +1055,7 @@ process bwa {
 }
 
 process circulargenerator{
+    label 'sc_tiny'
     tag "$prefix"
     publishDir "${params.outdir}/reference_genome/circularmapper_index", mode: 'copy', saveAs: { filename -> 
             if (params.saveReference) filename 
@@ -1053,7 +1066,7 @@ process circulargenerator{
     when: params.mapper == 'circularmapper' && !params.skip_mapping
 
     input:
-    file fasta from fasta_for_indexing
+    file fasta from ch_fasta_for_circulargenerator
 
     output:
     file "${prefix}.{amb,ann,bwt,sa,pac}" into ch_circularmapper_indices
@@ -1069,6 +1082,7 @@ process circulargenerator{
 
 
 process circularmapper{
+    label 'mc_medium'
     tag "$prefix"
     publishDir "${params.outdir}/mapping/circularmapper", mode: 'copy'
 
@@ -1077,7 +1091,7 @@ process circularmapper{
     input:
     set val(name), file(reads) from ch_adapteremoval_for_cm
     file index from ch_circularmapper_indices.collect()
-    file fasta from fasta_for_indexing
+    file fasta from ch_fasta_for_circularmapper.collect()
 
     output:
     file "*.mapped.bam" into ch_output_from_cm
@@ -1114,6 +1128,7 @@ process circularmapper{
 }
 
 process bwamem {
+    label 'mc_medium'
     tag "$prefix"
     publishDir "${params.outdir}/mapping/bwamem", mode: 'copy'
 
@@ -1171,6 +1186,7 @@ if (!params.skip_mapping) {
 */
 
 process samtools_flagstat {
+    label 'sc_tiny'
     tag "$prefix"
     publishDir "${params.outdir}/samtools/stats", mode: 'copy'
 
@@ -1196,6 +1212,7 @@ process samtools_flagstat {
 */
 
 process samtools_filter {
+    label 'mc_medium'
     tag "$prefix"
     publishDir "${params.outdir}/samtools/filter", mode: 'copy',
     saveAs: {filename ->
@@ -1228,19 +1245,22 @@ process samtools_filter {
         """
     } else if("${params.bam_discard_unmapped}" && "${params.bam_unmapped_type}" == "bam"){
         """
-        samtools view -h $bam | tee >(samtools view - -@ ${task.cpus} -f4 -q ${params.bam_mapping_quality_threshold} -o ${prefix}.unmapped.bam) >(samtools view - -@ ${task.cpus} -F4 -q ${params.bam_mapping_quality_threshold} -o ${prefix}.filtered.bam)
+        samtools view -h $bam | samtools view - -@ ${task.cpus} -f4 -q ${params.bam_mapping_quality_threshold} -o ${prefix}.unmapped.bam
+        samtools view -h $bam | samtools view - -@ ${task.cpus} -F4 -q ${params.bam_mapping_quality_threshold} -o ${prefix}.filtered.bam
         samtools index "${size}" ${prefix}.filtered.bam
         """
     } else if("${params.bam_discard_unmapped}" && "${params.bam_unmapped_type}" == "fastq"){
         """
-        samtools view -h $bam | tee >(samtools view - -@ ${task.cpus} -f4 -q ${params.bam_mapping_quality_threshold} -o ${prefix}.unmapped.bam) >(samtools view - -@ ${task.cpus} -F4 -q ${params.bam_mapping_quality_threshold} -o ${prefix}.filtered.bam)
+        samtools view -h $bam | samtools view - -@ ${task.cpus} -f4 -q ${params.bam_mapping_quality_threshold} -o ${prefix}.unmapped.bam
+        samtools view -h $bam | samtools view - -@ ${task.cpus} -F4 -q ${params.bam_mapping_quality_threshold} -o ${prefix}.filtered.bam
         samtools index "${size}" ${prefix}.filtered.bam
         samtools fastq -tn ${prefix}.unmapped.bam | pigz -p ${task.cpus} > ${prefix}.unmapped.fastq.gz
         rm ${prefix}.unmapped.bam
         """
     } else if("${params.bam_discard_unmapped}" && "${params.bam_unmapped_type}" == "both"){
         """
-        samtools view -h $bam | tee >(samtools view - -@ ${task.cpus} -f4 -q ${params.bam_mapping_quality_threshold} -o ${prefix}.unmapped.bam) >(samtools view - -@ ${task.cpus} -F4 -q ${params.bam_mapping_quality_threshold} -o ${prefix}.filtered.bam)
+        samtools view -h $bam | samtools view - -@ ${task.cpus} -f4 -q ${params.bam_mapping_quality_threshold} -o ${prefix}.unmapped.bam)
+        samtools view -h $bam | samtools view - -@ ${task.cpus} -F4 -q ${params.bam_mapping_quality_threshold} -o ${prefix}.filtered.bam)
         samtools index "${size}" ${prefix}.filtered.bam
         samtools fastq -tn ${prefix}.unmapped.bam | pigz -p ${task.cpus} > ${prefix}.unmapped.fastq.gz
         """
@@ -1276,6 +1296,7 @@ if (params.run_bam_filtering) {
 
 
 process strip_input_fastq {
+    label 'mc_medium'
     tag "${bam.baseName}"
     publishDir "${params.outdir}/samtools/stripped_fastq", mode: 'copy'
 
@@ -1314,6 +1335,7 @@ process strip_input_fastq {
 
 
 process samtools_flagstat_after_filter {
+    label 'sc_tiny'
     tag "$prefix"
     publishDir "${params.outdir}/samtools/stats", mode: 'copy'
 
@@ -1339,6 +1361,7 @@ Step 5a: DeDup
 */ 
 
 process dedup{
+    label 'mc_small'
     tag "${bam.baseName}"
     publishDir "${params.outdir}/deduplication/", mode: 'copy',
         saveAs: {filename -> "${prefix}/$filename"}
@@ -1382,6 +1405,7 @@ process dedup{
  */
 
 process markDup{
+    label 'mc_small'
     tag "${bam.baseName}"
     publishDir "${params.outdir}/deduplication/"
 
@@ -1430,6 +1454,7 @@ Step 6: Preseq
 */
 
 process preseq {
+    label 'sc_tiny'
     tag "${input.baseName}"
     publishDir "${params.outdir}/preseq", mode: 'copy'
 
@@ -1460,6 +1485,7 @@ Step 7a: DMG Assessment
 */ 
 
 process damageprofiler {
+    label 'sc_tiny'
     tag "${bam.baseName}"
     publishDir "${params.outdir}/damageprofiler", mode: 'copy'
 
@@ -1468,7 +1494,7 @@ process damageprofiler {
 
     input:
     file bam from ch_rmdup_for_damageprofiler
-    file fasta from fasta_for_indexing
+    file fasta from ch_fasta_for_damageprofiler.collect()
     file bai from ch_rmdupindex_for_damageprofiler
     
 
@@ -1490,6 +1516,7 @@ Step 8: Qualimap
 */
 
 process qualimap {
+    label 'mc_small'
     tag "${bam.baseName}"
     publishDir "${params.outdir}/qualimap", mode: 'copy'
 
@@ -1498,7 +1525,7 @@ process qualimap {
 
     input:
     file bam from ch_rmdup_for_qualimap
-    file fasta from fasta_for_indexing
+    file fasta from ch_fasta_for_qualimap.collect()
 
     output:
     file "*" into ch_qualimap_results
@@ -1525,6 +1552,7 @@ if (!params.run_bedtools_coverage){
 }
 
 process bedtools {
+  label 'mc_small'
   tag "${bam.baseName}"
   publishDir "${params.outdir}/bedtools", mode: 'copy'
 
@@ -1533,15 +1561,15 @@ process bedtools {
 
   input:
   file bam from ch_rmdup_for_bedtools
-  file anno_file from ch_anno_for_bedtools
+  file anno_file from ch_anno_for_bedtools.collect()
 
   output:
   file "*"
 
   script:
   """
-  bedtools coverage -a ${anno_file} -b $bam | pigz -p 4 > "${bam.baseName}".breadth.gz 
-  bedtools coverage -a ${anno_file} -b $bam -mean | pigz -p 4 > "${bam.baseName}".depth.gz 
+  bedtools coverage -a ${anno_file} -b $bam | pigz -p ${task.cpus} > "${bam.baseName}".breadth.gz
+  bedtools coverage -a ${anno_file} -b $bam -mean | pigz -p ${task.cpus} > "${bam.baseName}".depth.gz
   """
 }
 
@@ -1550,6 +1578,7 @@ process bedtools {
  */
 
 process pmdtools {
+    label 'mc_small'
     tag "${bam.baseName}"
     publishDir "${params.outdir}/pmdtools", mode: 'copy'
 
@@ -1557,7 +1586,7 @@ process pmdtools {
 
     input: 
     file bam from ch_rmdup_for_pmdtools
-    file fasta from fasta_for_indexing
+    file fasta from ch_fasta_for_pmdtools.collect()
 
     output:
     file "*.bam" into ch_output_from_pmdtools
@@ -1590,6 +1619,7 @@ process pmdtools {
 */
 
 process bam_trim {
+    label 'mc_small'
     tag "${prefix}" 
     publishDir "${params.outdir}/trimmed_bam", mode: 'copy'
  
@@ -1663,6 +1693,7 @@ if ( params.run_genotyping && params.genotyping_source == 'raw' ) {
 ch_gatk_download = Channel.value("download")
 
  process download_gatk_v3_5 {
+    label 'sc_tiny'
     when: params.run_genotyping && params.genotyping_tool == 'ug'
 
     input: 
@@ -1683,6 +1714,7 @@ ch_gatk_download = Channel.value("download")
 */
 
  process genotyping_ug {
+  label 'mc_small'
   tag "${prefix}"
   publishDir "${params.outdir}/genotyping", mode: 'copy'
 
@@ -1690,11 +1722,11 @@ ch_gatk_download = Channel.value("download")
   params.run_genotyping && params.genotyping_tool == 'ug'
 
   input:
-  file fasta from fasta_for_indexing
-  file jar from ch_unifiedgenotyper_jar
+  file fasta from ch_fasta_for_genotyping_ug.collect()
+  file jar from ch_unifiedgenotyper_jar.collect()
   file bam from ch_damagemanipulation_for_genotyping_ug
-  file fai from ch_fai_for_ug
-  file dict from ch_dict_for_ug
+  file fai from ch_fai_for_ug.collect()
+  file dict from ch_dict_for_ug.collect()
 
   output: 
   file "*vcf.gz" into ch_ug_for_multivcfanalyzer,ch_ug_for_vcf2genome
@@ -1705,23 +1737,23 @@ ch_gatk_download = Channel.value("download")
   if (params.gatk_dbsnp == '')
     """
     samtools index -b ${bam}
-    java -jar ${jar} -T RealignerTargetCreator -R ${fasta} -I ${bam} -nt ${task.cpus} -o ${bam}.intervals 
-    java -jar ${jar} -T IndelRealigner -R ${fasta} -I ${bam} -targetIntervals ${bam}.intervals -o ${bam}.realign.bam
-    java -jar ${jar} -T UnifiedGenotyper -R ${fasta} -I ${bam}.realign.bam -o ${bam}.unifiedgenotyper.vcf -nt ${task.cpus} --genotype_likelihoods_model ${params.gatk_ug_genotype_model} -stand_call_conf ${params.gatk_call_conf} --sample_ploidy ${params.gatk_ploidy} -dcov ${params.gatk_downsample} --output_mode ${params.gatk_ug_out_mode} ${defaultbasequalities}
+    java -Xmx${task.memory.toGiga()}g -jar ${jar} -T RealignerTargetCreator -R ${fasta} -I ${bam} -nt ${task.cpus} -o ${bam}.intervals ${defaultbasequalities}
+    java -Xmx${task.memory.toGiga()}g -jar ${jar} -T IndelRealigner -R ${fasta} -I ${bam} -targetIntervals ${bam}.intervals -o ${bam}.realign.bam ${defaultbasequalities}
+    java -Xmx${task.memory.toGiga()}g -jar ${jar} -T UnifiedGenotyper -R ${fasta} -I ${bam}.realign.bam -o ${bam}.unifiedgenotyper.vcf -nt ${task.cpus} --genotype_likelihoods_model ${params.gatk_ug_genotype_model} -stand_call_conf ${params.gatk_call_conf} --sample_ploidy ${params.gatk_ploidy} -dcov ${params.gatk_downsample} --output_mode ${params.gatk_ug_out_mode} ${defaultbasequalities}
     pigz -p ${task.cpus} ${bam}.unifiedgenotyper.vcf
     """
   else if (params.gatk_dbsnp != '')
     """
     samtools index ${bam}
-    java -jar ${jar} -T RealignerTargetCreator -R ${fasta} -I ${bam} -nt ${task.cpus} -o ${bam}.intervals 
-    java -jar ${jar} -T IndelRealigner -R ${fasta} -I ${bam} -targetIntervals ${bam}.intervals -o ${bam}.realign.bam
+    java -jar ${jar} -T RealignerTargetCreator -R ${fasta} -I ${bam} -nt ${task.cpus} -o ${bam}.intervals ${defaultbasequalities}
+    java -jar ${jar} -T IndelRealigner -R ${fasta} -I ${bam} -targetIntervals ${bam}.intervals -o ${bam}.realign.bam ${defaultbasequalities}
     java -jar ${jar} -T UnifiedGenotyper -R ${fasta} -I ${bam}.realign.bam -o ${bam}.unifiedgenotyper.vcf -nt ${task.cpus} --dbsnp ${params.gatk_dbsnp} --genotype_likelihoods_model ${params.gatk_ug_genotype_model} -stand_call_conf ${params.gatk_call_conf} --sample_ploidy ${params.gatk_ploidy} -dcov ${params.gatk_downsample} --output_mode ${params.gatk_ug_out_mode} ${defaultbasequalities}
-
     pigz -p ${task.cpus} ${bam}.unifiedgenotyper.vcf
     """
  }
 
   process genotyping_hc {
+  label 'mc_small'
   tag "${prefix}"
   publishDir "${params.outdir}/genotyping", mode: 'copy'
 
@@ -1729,11 +1761,11 @@ ch_gatk_download = Channel.value("download")
   params.run_genotyping && params.genotyping_tool == 'hc'
 
   input:
-  file fasta from fasta_for_indexing
+  file fasta from ch_fasta_for_genotyping_hc.collect()
   file bam from ch_damagemanipulation_for_genotyping_hc
-  file fai from ch_fai_for_hc
-  file dict from ch_dict_for_hc
-  file bai from ch_damagemanipulationindex_for_genotyping_hc
+  file fai from ch_fai_for_hc.collect()
+  file dict from ch_dict_for_hc.collect()
+  file bai from ch_damagemanipulationindex_for_genotyping_hc.collect()
 
   output: 
   file "*vcf.gz" into ch_vcf_hc
@@ -1757,6 +1789,7 @@ ch_gatk_download = Channel.value("download")
  *  Step 12c: FreeBayes genotyping, should probably add in some options for users to set 
  */ 
  process genotyping_freebayes {
+  label 'mc_small'
   tag "${prefix}"
   publishDir "${params.outdir}/genotyping", mode: 'copy'
 
@@ -1764,11 +1797,11 @@ ch_gatk_download = Channel.value("download")
   params.run_genotyping && params.genotyping_tool == 'freebayes'
 
   input:
-  file fasta from fasta_for_indexing
+  file fasta from ch_fasta_for_genotyping_freebayes.collect()
   file bam from ch_damagemanipulation_for_genotyping_freebayes
-  file fai from ch_fai_for_freebayes
-  file dict from ch_dict_for_freebayes
-  file bai from ch_damagemanipulationindex_for_genotyping_freebayes
+  file fai from ch_fai_for_freebayes.collect()
+  file dict from ch_dict_for_freebayes.collect()
+  file bai from ch_damagemanipulationindex_for_genotyping_freebayes.collect()
 
   output: 
   file "*vcf.gz" into ch_vcf_freebayes
@@ -1782,13 +1815,12 @@ ch_gatk_download = Channel.value("download")
   """
  }
 
-
 /*
  * Step 13: VCF2Genome
 */
 
-
 process vcf2genome {
+  label  'mc_small'
   tag "${prefix}"
   publishDir "${params.outdir}/consensus_sequence", mode: 'copy'
 
@@ -1797,7 +1829,7 @@ process vcf2genome {
 
   input:
   file vcf from ch_ug_for_vcf2genome
-  file fasta from fasta_for_indexing
+  file fasta from ch_fasta_for_vcf2genome.collect()
 
   output:
   file "*.fasta.gz"
@@ -1828,14 +1860,15 @@ if (params.additional_vcf_files == '') {
 }
 
  process multivcfanalyzer {
+  label  'mc_small'
   publishDir "${params.outdir}/MultiVCFAnalyzer", mode: 'copy'
 
   when:
   params.genotyping_tool == 'ug' && params.run_multivcfanalyzer && params.gatk_ploidy == '2'
 
   input:
-  file fasta from fasta_for_indexing
-  file vcf from ch_vcfs_for_multivcfanalyzer
+  file fasta from ch_fasta_for_multivcfanalyzer.collect()
+  file vcf from ch_vcfs_for_multivcfanalyzer.collect()
 
   output:
   file 'fullAlignment.fasta.gz' into ch_output_multivcfanalyzer_fullalignment
@@ -1897,7 +1930,8 @@ if (params.sexdeterrmine_bedfile == '') {
 
 
  process sex_deterrmine {
-     publishDir "${params.outdir}/sex_determination", mode:"copy"
+    label 'sc_small'
+    publishDir "${params.outdir}/sex_determination", mode:"copy"
     
      when:
      params.run_sexdeterrmine
@@ -1934,47 +1968,48 @@ if (params.sexdeterrmine_bedfile == '') {
   * Step 16 Nuclear contamination for Human DNA based on chromosome X heterozygosity.
   */
  process nuclear_contamination{
-     publishDir "${params.outdir}/nuclear_contamination", mode:"copy"
-     validExitStatus 0,134
-     /* 
-      * ANGSD Xcontamination will exit with status 134 when the number of SNPs 
-      *     is not large enough for estimation.
-      */
-     
-     when:
-     params.run_nuclear_contamination
-    
-     input:
-     file input from ch_for_nuclear_contamination
-    
-    
-     output:
-     file '*.X.contamination.out' into ch_from_nuclear_contamination
-     
-     script:
-     """
-     samtools index ${input}
-     angsd -i ${input} -r ${params.contamination_chrom_name}:5000000-154900000 -doCounts 1 -iCounts 1 -minMapQ 30 -minQ 30 -out ${input.baseName}.doCounts
-     contamination -a ${input.baseName}.doCounts.icnts.gz -h ${baseDir}/assets/angsd_resources/HapMapChrX.gz 2> ${input.baseName}.X.contamination.out
-     """
+    label 'sc_small'
+    publishDir "${params.outdir}/nuclear_contamination", mode:"copy"
+    validExitStatus 0,134
+    /*
+     * ANGSD Xcontamination will exit with status 134 when the number of SNPs
+     *     is not large enough for estimation.
+     */
+
+    when:
+    params.run_nuclear_contamination
+
+    input:
+    file input from ch_for_nuclear_contamination
+
+    output:
+    file '*.X.contamination.out' into ch_from_nuclear_contamination
+
+    script:
+    """
+    samtools index ${input}
+    angsd -i ${input} -r ${params.contamination_chrom_name}:5000000-154900000 -doCounts 1 -iCounts 1 -minMapQ 30 -minQ 30 -out ${input.baseName}.doCounts
+    contamination -a ${input.baseName}.doCounts.icnts.gz -h ${baseDir}/assets/angsd_resources/HapMapChrX.gz 2> ${input.baseName}.X.contamination.out
+    """
  }
  
- process print_nuclear_contamination{
-     publishDir "${params.outdir}/nuclear_contamination", mode:"copy"
-     
-     when:
-     params.run_nuclear_contamination
-    
-     input:
-     val 'Contam' from ch_from_nuclear_contamination.collect()
-    
-     output:
-     file 'nuclear_contamination.txt'
-     
-     script:
-     """
-     print_x_contamination.py ${Contam.join(' ')}
-     """
+process print_nuclear_contamination{
+    label 'sc_tiny'
+    publishDir "${params.outdir}/nuclear_contamination", mode:"copy"
+
+    when:
+    params.run_nuclear_contamination
+
+    input:
+    val 'Contam' from ch_from_nuclear_contamination.collect()
+
+    output:
+    file 'nuclear_contamination.txt'
+
+    script:
+    """
+    print_x_contamination.py ${Contam.join(' ')}
+    """
  }
 
 /*
@@ -1982,6 +2017,7 @@ if (params.sexdeterrmine_bedfile == '') {
 */
 
 process malt {
+  label 'mc_huge'
   publishDir "${params.outdir}/metagenomic_classification", mode:"copy"
 
   when:
@@ -2041,6 +2077,7 @@ if (params.maltextract_taxon_list== '') {
 }
 
 process maltextract {
+  label 'mc_large'
   publishDir "${params.outdir}/MaltExtract/", mode:"copy"
 
   when: 
@@ -2090,9 +2127,8 @@ Genotyping tools:
 - sequenceTools
 
 Downstream VCF tools:
-- vcf2genome
-- gencons
-- READ/mcMLKin
+- gencons?
+- READ/mcMLKin?
 - popGen output? PLINK? 
 */
 
@@ -2100,6 +2136,7 @@ Downstream VCF tools:
  * Step 18a - Output Description HTML
  */
 process output_documentation {
+    label 'sc_tiny'
     publishDir "${params.outdir}/Documentation", mode: 'copy'
 
     input:
@@ -2118,6 +2155,7 @@ process output_documentation {
  * Step 18b - Parse software version numbers
  */
 process get_software_versions {
+  label 'sc_tiny'
   publishDir "${params.outdir}/SoftwareVersions", mode: 'copy'
 
     output:
@@ -2163,6 +2201,8 @@ process get_software_versions {
  * Step 18c - MultiQC
  */
 process multiqc {
+    label 'sc_tiny'
+
     publishDir "${params.outdir}/MultiQC", mode: 'copy'
 
     input: